Starting phenix.real_space_refine on Wed Apr 10 10:29:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/04_2024/8kg6_37211_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/04_2024/8kg6_37211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/04_2024/8kg6_37211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/04_2024/8kg6_37211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/04_2024/8kg6_37211_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/04_2024/8kg6_37211_updated.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 70 5.49 5 Mg 5 5.21 5 S 310 5.16 5 C 44722 2.51 5 N 12061 2.21 5 O 13438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 184": "OE1" <-> "OE2" Residue "2 TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 413": "OD1" <-> "OD2" Residue "2 GLU 468": "OE1" <-> "OE2" Residue "4 ASP 569": "OD1" <-> "OD2" Residue "5 ASP 336": "OD1" <-> "OD2" Residue "5 GLU 338": "OE1" <-> "OE2" Residue "5 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 736": "OE1" <-> "OE2" Residue "5 PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 743": "OE1" <-> "OE2" Residue "7 TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 250": "OD1" <-> "OD2" Residue "7 PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 706": "OD1" <-> "OD2" Residue "7 TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 824": "OE1" <-> "OE2" Residue "K GLU 412": "OE1" <-> "OE2" Residue "K PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 1412": "OE1" <-> "OE2" Residue "M GLU 1801": "OE1" <-> "OE2" Residue "M TYR 1881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 2084": "OE1" <-> "OE2" Residue "N TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 473": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 70613 Number of models: 1 Model: "" Number of chains: 27 Chain: "2" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5245 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 636} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5005 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 29, 'TRANS': 615} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "4" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5494 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 23, 'TRANS': 672} Chain breaks: 5 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "5" Number of atoms: 5334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5334 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 26, 'TRANS': 650} Chain breaks: 6 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "6" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4880 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 596} Chain breaks: 6 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "7" Number of atoms: 5023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5023 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 30, 'TRANS': 616} Chain breaks: 6 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1625 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1630 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain breaks: 1 Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1394 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2004 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 2 Chain: "E" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4591 Classifications: {'peptide': 568} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 552} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3467 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3362 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3358 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 722 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 438 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "K" Number of atoms: 5350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5350 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 639} Chain breaks: 7 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 788 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "M" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6490 Classifications: {'peptide': 813} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 29, 'TRANS': 783} Chain breaks: 6 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "N" Number of atoms: 4254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4254 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 30, 'TRANS': 505} Chain breaks: 5 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1311 SG CYS 2 341 91.897 160.539 137.536 1.00153.63 S ATOM 1334 SG CYS 2 344 92.545 163.894 138.191 1.00159.01 S ATOM 1492 SG CYS 2 364 95.627 160.829 138.766 1.00160.53 S ATOM 11648 SG CYS 4 349 104.539 156.837 175.423 1.00186.60 S ATOM 11669 SG CYS 4 352 107.704 157.643 177.327 1.00202.71 S ATOM 11816 SG CYS 4 371 104.315 158.571 178.805 1.00219.14 S ATOM 11858 SG CYS 4 376 105.748 160.465 175.846 1.00235.75 S ATOM 16884 SG CYS 5 183 67.104 160.118 139.094 1.00107.24 S ATOM 16909 SG CYS 5 186 65.273 163.289 138.503 1.00112.73 S ATOM 17073 SG CYS 5 211 68.943 163.526 138.513 1.00112.92 S ATOM 17110 SG CYS 5 236 67.373 162.812 141.804 1.00122.35 S ATOM 22306 SG CYS 6 311 108.480 157.777 152.137 1.00161.60 S ATOM 22328 SG CYS 6 314 109.321 161.325 151.410 1.00168.39 S ATOM 22485 SG CYS 6 333 108.706 160.246 155.063 1.00189.41 S ATOM 22519 SG CYS 6 338 105.844 160.521 152.596 1.00185.49 S ATOM 27551 SG CYS 7 262 76.725 156.156 183.223 1.00202.99 S ATOM 27724 SG CYS 7 284 74.839 158.131 182.583 1.00221.60 S ATOM 27761 SG CYS 7 289 76.704 160.520 182.003 1.00254.18 S ATOM 65286 SG CYS M2108 96.942 48.673 69.063 1.00120.64 S ATOM 65313 SG CYS M2111 98.826 46.173 71.235 1.00122.53 S ATOM 65462 SG CYS M2130 99.694 49.751 71.447 1.00114.26 S ATOM 65486 SG CYS M2133 100.623 47.823 68.309 1.00116.36 S ATOM 65749 SG CYS M2164 75.763 77.695 100.085 1.00 73.50 S ATOM 65772 SG CYS M2167 75.485 75.026 102.819 1.00 75.91 S ATOM 65873 SG CYS M2179 72.342 76.306 101.102 1.00 69.00 S ATOM 65886 SG CYS M2181 74.362 78.530 103.451 1.00 67.20 S Time building chain proxies: 27.44, per 1000 atoms: 0.39 Number of scatterers: 70613 At special positions: 0 Unit cell: (173.84, 244.86, 231.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 310 16.00 P 70 15.00 Mg 5 11.99 O 13438 8.00 N 12061 7.00 C 44722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.82 Conformation dependent library (CDL) restraints added in 9.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 364 " pdb=" ZN 41400 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 349 " pdb=" ZN 5 801 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 211 " pdb=" ZN 61101 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 289 " pdb=" ZN M3001 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2111 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2130 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2133 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2108 " pdb=" ZN M3002 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2181 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2164 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2167 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2179 " Number of angles added : 30 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16596 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 317 helices and 81 sheets defined 40.9% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.95 Creating SS restraints... Processing helix chain '2' and resid 183 through 187 Processing helix chain '2' and resid 194 through 199 Processing helix chain '2' and resid 201 through 217 Processing helix chain '2' and resid 226 through 236 Processing helix chain '2' and resid 246 through 251 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 264 through 282 removed outlier: 3.911A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 288 No H-bonds generated for 'chain '2' and resid 286 through 288' Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 478 through 488 Processing helix chain '2' and resid 493 through 499 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 573 through 576 No H-bonds generated for 'chain '2' and resid 573 through 576' Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 614 through 625 removed outlier: 4.709A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE 2 620 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS 2 621 " --> pdb=" O ARG 2 617 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLU 2 622 " --> pdb=" O THR 2 618 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA 2 623 " --> pdb=" O SER 2 619 " (cutoff:3.500A) Processing helix chain '2' and resid 653 through 655 No H-bonds generated for 'chain '2' and resid 653 through 655' Processing helix chain '2' and resid 663 through 665 No H-bonds generated for 'chain '2' and resid 663 through 665' Processing helix chain '2' and resid 671 through 674 No H-bonds generated for 'chain '2' and resid 671 through 674' Processing helix chain '2' and resid 689 through 705 Processing helix chain '2' and resid 740 through 755 removed outlier: 3.862A pdb=" N GLU 2 754 " --> pdb=" O LYS 2 750 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE 2 755 " --> pdb=" O LYS 2 751 " (cutoff:3.500A) Processing helix chain '2' and resid 760 through 773 removed outlier: 4.009A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 783 through 798 Processing helix chain '2' and resid 807 through 823 removed outlier: 3.754A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 848 removed outlier: 3.611A pdb=" N ALA 2 837 " --> pdb=" O ASP 2 833 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) Processing helix chain '2' and resid 851 through 864 removed outlier: 4.620A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N TYR 2 864 " --> pdb=" O SER 2 860 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 34 Processing helix chain '3' and resid 36 through 54 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 135 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 262 through 264 No H-bonds generated for 'chain '3' and resid 262 through 264' Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 355 removed outlier: 3.639A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 365 Processing helix chain '3' and resid 375 through 385 Processing helix chain '3' and resid 415 through 425 removed outlier: 3.687A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) Processing helix chain '3' and resid 439 through 443 Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 482 No H-bonds generated for 'chain '3' and resid 480 through 482' Processing helix chain '3' and resid 484 through 492 Processing helix chain '3' and resid 537 through 542 removed outlier: 4.782A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) Processing helix chain '3' and resid 556 through 570 Processing helix chain '3' and resid 653 through 666 Processing helix chain '3' and resid 673 through 687 removed outlier: 3.781A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 700 through 715 Processing helix chain '3' and resid 723 through 737 Processing helix chain '4' and resid 187 through 198 Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 246 through 250 Processing helix chain '4' and resid 255 through 263 Processing helix chain '4' and resid 265 through 287 Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 314 through 316 No H-bonds generated for 'chain '4' and resid 314 through 316' Processing helix chain '4' and resid 386 through 388 No H-bonds generated for 'chain '4' and resid 386 through 388' Processing helix chain '4' and resid 503 through 513 Processing helix chain '4' and resid 518 through 526 Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 573 through 584 removed outlier: 4.628A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 610 through 612 No H-bonds generated for 'chain '4' and resid 610 through 612' Processing helix chain '4' and resid 639 through 651 Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 701 removed outlier: 3.662A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 730 removed outlier: 3.772A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) Processing helix chain '4' and resid 746 through 757 removed outlier: 4.190A pdb=" N SER 4 752 " --> pdb=" O THR 4 748 " (cutoff:3.500A) Processing helix chain '4' and resid 764 through 779 Processing helix chain '4' and resid 795 through 810 removed outlier: 3.516A pdb=" N GLU 4 806 " --> pdb=" O ILE 4 802 " (cutoff:3.500A) Processing helix chain '4' and resid 819 through 836 removed outlier: 3.557A pdb=" N GLN 4 823 " --> pdb=" O LEU 4 819 " (cutoff:3.500A) Processing helix chain '4' and resid 852 through 873 removed outlier: 4.489A pdb=" N ILE 4 857 " --> pdb=" O GLY 4 853 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN 4 858 " --> pdb=" O LYS 4 854 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU 4 863 " --> pdb=" O ARG 4 859 " (cutoff:3.500A) Processing helix chain '4' and resid 883 through 888 Processing helix chain '4' and resid 900 through 912 removed outlier: 3.823A pdb=" N GLN 4 904 " --> pdb=" O SER 4 900 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG 4 909 " --> pdb=" O GLU 4 905 " (cutoff:3.500A) Processing helix chain '5' and resid 21 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 102 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 148 through 150 No H-bonds generated for 'chain '5' and resid 148 through 150' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 366 through 372 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 446 through 449 No H-bonds generated for 'chain '5' and resid 446 through 449' Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 482 through 484 No H-bonds generated for 'chain '5' and resid 482 through 484' Processing helix chain '5' and resid 487 through 498 removed outlier: 3.785A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS 5 494 " --> pdb=" O ARG 5 490 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 536 through 539 No H-bonds generated for 'chain '5' and resid 536 through 539' Processing helix chain '5' and resid 544 through 549 removed outlier: 3.778A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 579 through 590 removed outlier: 4.078A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) Processing helix chain '5' and resid 596 through 609 removed outlier: 3.799A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) Processing helix chain '5' and resid 616 through 640 Processing helix chain '5' and resid 650 through 667 removed outlier: 3.868A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 692 removed outlier: 4.018A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) Processing helix chain '5' and resid 708 through 721 Processing helix chain '5' and resid 730 through 736 Processing helix chain '5' and resid 750 through 758 Processing helix chain '6' and resid 106 through 120 Processing helix chain '6' and resid 135 through 146 Processing helix chain '6' and resid 155 through 172 removed outlier: 5.069A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN 6 163 " --> pdb=" O SER 6 159 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY 6 164 " --> pdb=" O MET 6 160 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA 6 165 " --> pdb=" O ARG 6 161 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU 6 166 " --> pdb=" O GLU 6 162 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA 6 167 " --> pdb=" O ASN 6 163 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 192 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 365 through 367 No H-bonds generated for 'chain '6' and resid 365 through 367' Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 407 through 410 No H-bonds generated for 'chain '6' and resid 407 through 410' Processing helix chain '6' and resid 501 through 507 Processing helix chain '6' and resid 510 through 520 Processing helix chain '6' and resid 525 through 531 Processing helix chain '6' and resid 541 through 552 Processing helix chain '6' and resid 581 through 591 Processing helix chain '6' and resid 627 through 630 No H-bonds generated for 'chain '6' and resid 627 through 630' Processing helix chain '6' and resid 646 through 657 removed outlier: 4.970A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE 6 652 " --> pdb=" O ASP 6 648 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS 6 653 " --> pdb=" O GLN 6 649 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU 6 657 " --> pdb=" O HIS 6 653 " (cutoff:3.500A) Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 706 No H-bonds generated for 'chain '6' and resid 703 through 706' Processing helix chain '6' and resid 721 through 736 removed outlier: 3.743A pdb=" N THR 6 725 " --> pdb=" O GLU 6 721 " (cutoff:3.500A) Processing helix chain '6' and resid 748 through 760 removed outlier: 3.813A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR 6 754 " --> pdb=" O GLN 6 750 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 783 removed outlier: 3.592A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 813 Processing helix chain '6' and resid 821 through 834 removed outlier: 3.803A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) Processing helix chain '7' and resid 14 through 26 Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 82 through 93 Processing helix chain '7' and resid 102 through 106 Processing helix chain '7' and resid 110 through 123 removed outlier: 3.601A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 138 through 154 removed outlier: 4.008A pdb=" N MET 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 194 through 197 No H-bonds generated for 'chain '7' and resid 194 through 197' Processing helix chain '7' and resid 213 through 215 No H-bonds generated for 'chain '7' and resid 213 through 215' Processing helix chain '7' and resid 227 through 229 No H-bonds generated for 'chain '7' and resid 227 through 229' Processing helix chain '7' and resid 232 through 234 No H-bonds generated for 'chain '7' and resid 232 through 234' Processing helix chain '7' and resid 287 through 292 Processing helix chain '7' and resid 364 through 368 Processing helix chain '7' and resid 396 through 407 Processing helix chain '7' and resid 410 through 418 removed outlier: 4.104A pdb=" N ALA 7 415 " --> pdb=" O TYR 7 411 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS 7 416 " --> pdb=" O ASN 7 412 " (cutoff:3.500A) Processing helix chain '7' and resid 426 through 437 Processing helix chain '7' and resid 466 through 476 Processing helix chain '7' and resid 531 through 543 Processing helix chain '7' and resid 580 through 583 No H-bonds generated for 'chain '7' and resid 580 through 583' Processing helix chain '7' and resid 588 through 592 Processing helix chain '7' and resid 608 through 622 Processing helix chain '7' and resid 636 through 648 removed outlier: 4.077A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 674 Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 728 removed outlier: 3.561A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 21 Processing helix chain 'A' and resid 34 through 60 Processing helix chain 'A' and resid 65 through 104 removed outlier: 3.692A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.622A pdb=" N ASP A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.715A pdb=" N ASN B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 138 through 157 removed outlier: 3.793A pdb=" N GLY B 143 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 Proline residue: B 183 - end of helix removed outlier: 3.839A pdb=" N GLU B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 48 through 54 removed outlier: 4.346A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 118 through 139 removed outlier: 3.696A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU C 126 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.742A pdb=" N LEU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 191 removed outlier: 3.528A pdb=" N LYS C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 12 Processing helix chain 'D' and resid 56 through 72 removed outlier: 3.597A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 106 Processing helix chain 'D' and resid 124 through 153 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 177 through 197 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 279 through 287 removed outlier: 4.886A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 19 Processing helix chain 'E' and resid 36 through 51 Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 100 through 102 No H-bonds generated for 'chain 'E' and resid 100 through 102' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 148 through 151 No H-bonds generated for 'chain 'E' and resid 148 through 151' Processing helix chain 'E' and resid 153 through 165 Processing helix chain 'E' and resid 224 through 240 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 267 through 280 removed outlier: 4.016A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 302 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 366 removed outlier: 3.973A pdb=" N LYS E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 373 No H-bonds generated for 'chain 'E' and resid 370 through 373' Processing helix chain 'E' and resid 382 through 394 removed outlier: 3.564A pdb=" N GLU E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 421 through 434 Processing helix chain 'E' and resid 465 through 484 removed outlier: 3.624A pdb=" N PHE E 477 " --> pdb=" O TRP E 473 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 484 " --> pdb=" O SER E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 516 removed outlier: 3.698A pdb=" N ARG E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 540 removed outlier: 3.840A pdb=" N ARG E 540 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 557 Processing helix chain 'E' and resid 595 through 598 No H-bonds generated for 'chain 'E' and resid 595 through 598' Processing helix chain 'E' and resid 605 through 614 Processing helix chain 'E' and resid 636 through 646 Processing helix chain 'F' and resid 673 through 679 Processing helix chain 'F' and resid 724 through 732 Processing helix chain 'F' and resid 783 through 788 removed outlier: 4.221A pdb=" N GLU F 788 " --> pdb=" O SER F 784 " (cutoff:3.500A) Processing helix chain 'F' and resid 819 through 842 removed outlier: 3.996A pdb=" N GLU F 824 " --> pdb=" O SER F 820 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 840 " --> pdb=" O LEU F 836 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 842 " --> pdb=" O THR F 838 " (cutoff:3.500A) Processing helix chain 'F' and resid 851 through 876 removed outlier: 3.513A pdb=" N ASP F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 879 through 888 removed outlier: 3.621A pdb=" N HIS F 887 " --> pdb=" O LEU F 883 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU F 888 " --> pdb=" O SER F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 892 through 904 Processing helix chain 'F' and resid 908 through 923 removed outlier: 4.082A pdb=" N LYS F 912 " --> pdb=" O PRO F 908 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS F 913 " --> pdb=" O SER F 909 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU F 923 " --> pdb=" O GLU F 919 " (cutoff:3.500A) Processing helix chain 'G' and resid 674 through 679 Processing helix chain 'G' and resid 724 through 732 removed outlier: 4.299A pdb=" N SER G 732 " --> pdb=" O ILE G 728 " (cutoff:3.500A) Processing helix chain 'G' and resid 783 through 786 No H-bonds generated for 'chain 'G' and resid 783 through 786' Processing helix chain 'G' and resid 819 through 843 removed outlier: 3.837A pdb=" N ALA G 823 " --> pdb=" O VAL G 819 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU G 835 " --> pdb=" O LYS G 831 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR G 840 " --> pdb=" O LEU G 836 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU G 841 " --> pdb=" O LEU G 837 " (cutoff:3.500A) Processing helix chain 'G' and resid 851 through 875 Processing helix chain 'G' and resid 879 through 888 removed outlier: 4.213A pdb=" N GLU G 888 " --> pdb=" O SER G 884 " (cutoff:3.500A) Processing helix chain 'G' and resid 892 through 902 Processing helix chain 'G' and resid 908 through 921 removed outlier: 3.797A pdb=" N LYS G 912 " --> pdb=" O PRO G 908 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS G 913 " --> pdb=" O SER G 909 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE G 914 " --> pdb=" O LEU G 910 " (cutoff:3.500A) Processing helix chain 'H' and resid 674 through 679 Processing helix chain 'H' and resid 724 through 732 removed outlier: 3.853A pdb=" N TRP H 729 " --> pdb=" O ASN H 725 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS H 730 " --> pdb=" O MET H 726 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET H 731 " --> pdb=" O GLU H 727 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER H 732 " --> pdb=" O ILE H 728 " (cutoff:3.500A) Processing helix chain 'H' and resid 819 through 842 removed outlier: 3.703A pdb=" N GLU H 824 " --> pdb=" O SER H 820 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU H 835 " --> pdb=" O LYS H 831 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU H 836 " --> pdb=" O VAL H 832 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR H 840 " --> pdb=" O LEU H 836 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU H 841 " --> pdb=" O LEU H 837 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU H 842 " --> pdb=" O THR H 838 " (cutoff:3.500A) Processing helix chain 'H' and resid 851 through 876 Processing helix chain 'H' and resid 879 through 887 removed outlier: 3.760A pdb=" N HIS H 887 " --> pdb=" O LEU H 883 " (cutoff:3.500A) Processing helix chain 'H' and resid 892 through 902 Processing helix chain 'H' and resid 908 through 922 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 51 through 66 Processing helix chain 'K' and resid 74 through 80 Processing helix chain 'K' and resid 83 through 86 No H-bonds generated for 'chain 'K' and resid 83 through 86' Processing helix chain 'K' and resid 88 through 105 removed outlier: 3.577A pdb=" N LEU K 92 " --> pdb=" O LEU K 88 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN K 97 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 136 removed outlier: 3.523A pdb=" N ILE K 124 " --> pdb=" O TYR K 120 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA K 125 " --> pdb=" O TYR K 121 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN K 127 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS K 128 " --> pdb=" O ILE K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 168 removed outlier: 4.077A pdb=" N GLY K 154 " --> pdb=" O ILE K 150 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU K 155 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS K 158 " --> pdb=" O GLY K 154 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 173 No H-bonds generated for 'chain 'K' and resid 171 through 173' Processing helix chain 'K' and resid 175 through 187 removed outlier: 3.621A pdb=" N ARG K 181 " --> pdb=" O ARG K 177 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA K 183 " --> pdb=" O ALA K 179 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL K 186 " --> pdb=" O LEU K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 213 removed outlier: 3.638A pdb=" N LEU K 202 " --> pdb=" O ASP K 198 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS K 203 " --> pdb=" O ASN K 199 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE K 208 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE K 209 " --> pdb=" O VAL K 205 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG K 210 " --> pdb=" O LEU K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 248 No H-bonds generated for 'chain 'K' and resid 245 through 248' Processing helix chain 'K' and resid 250 through 259 Processing helix chain 'K' and resid 262 through 272 removed outlier: 3.513A pdb=" N THR K 270 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 289 Proline residue: K 285 - end of helix removed outlier: 4.011A pdb=" N GLU K 288 " --> pdb=" O ILE K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 294 No H-bonds generated for 'chain 'K' and resid 292 through 294' Processing helix chain 'K' and resid 300 through 302 No H-bonds generated for 'chain 'K' and resid 300 through 302' Processing helix chain 'K' and resid 330 through 351 removed outlier: 4.332A pdb=" N GLU K 334 " --> pdb=" O SER K 330 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS K 351 " --> pdb=" O LYS K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 360 No H-bonds generated for 'chain 'K' and resid 358 through 360' Processing helix chain 'K' and resid 385 through 394 Processing helix chain 'K' and resid 418 through 420 No H-bonds generated for 'chain 'K' and resid 418 through 420' Processing helix chain 'K' and resid 431 through 460 removed outlier: 3.601A pdb=" N ILE K 441 " --> pdb=" O PHE K 437 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN K 442 " --> pdb=" O LYS K 438 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE K 449 " --> pdb=" O ILE K 445 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASN K 450 " --> pdb=" O ASP K 446 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE K 451 " --> pdb=" O SER K 447 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN K 458 " --> pdb=" O HIS K 454 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR K 459 " --> pdb=" O SER K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 492 removed outlier: 3.507A pdb=" N VAL K 473 " --> pdb=" O THR K 469 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU K 477 " --> pdb=" O VAL K 473 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE K 478 " --> pdb=" O GLU K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 504 removed outlier: 3.502A pdb=" N SER K 502 " --> pdb=" O LYS K 499 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU K 503 " --> pdb=" O GLN K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 507 through 522 removed outlier: 3.599A pdb=" N TYR K 521 " --> pdb=" O LEU K 517 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP K 522 " --> pdb=" O ARG K 518 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 548 removed outlier: 3.543A pdb=" N ILE K 534 " --> pdb=" O HIS K 530 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA K 535 " --> pdb=" O ALA K 531 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU K 538 " --> pdb=" O ILE K 534 " (cutoff:3.500A) Processing helix chain 'K' and resid 557 through 561 removed outlier: 4.091A pdb=" N VAL K 561 " --> pdb=" O ILE K 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 557 through 561' Processing helix chain 'K' and resid 568 through 582 removed outlier: 4.525A pdb=" N LEU K 572 " --> pdb=" O GLU K 568 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU K 576 " --> pdb=" O LEU K 572 " (cutoff:3.500A) Proline residue: K 577 - end of helix removed outlier: 4.245A pdb=" N SER K 581 " --> pdb=" O PRO K 577 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS K 582 " --> pdb=" O LYS K 578 " (cutoff:3.500A) Processing helix chain 'K' and resid 585 through 604 removed outlier: 3.799A pdb=" N CYS K 591 " --> pdb=" O PHE K 587 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE K 592 " --> pdb=" O MET K 588 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU K 602 " --> pdb=" O VAL K 598 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU K 603 " --> pdb=" O LEU K 599 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN K 604 " --> pdb=" O LYS K 600 " (cutoff:3.500A) Processing helix chain 'K' and resid 659 through 662 No H-bonds generated for 'chain 'K' and resid 659 through 662' Processing helix chain 'K' and resid 669 through 681 removed outlier: 3.814A pdb=" N PHE K 678 " --> pdb=" O THR K 674 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU K 679 " --> pdb=" O TYR K 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU K 680 " --> pdb=" O ILE K 676 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG K 681 " --> pdb=" O ASN K 677 " (cutoff:3.500A) Processing helix chain 'K' and resid 687 through 698 removed outlier: 3.545A pdb=" N VAL K 693 " --> pdb=" O SER K 689 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE K 697 " --> pdb=" O VAL K 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 710 Processing helix chain 'K' and resid 713 through 723 Processing helix chain 'K' and resid 735 through 754 Processing helix chain 'K' and resid 758 through 762 Processing helix chain 'K' and resid 771 through 776 removed outlier: 3.764A pdb=" N PHE K 775 " --> pdb=" O SER K 771 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 60 No H-bonds generated for 'chain 'L' and resid 58 through 60' Processing helix chain 'L' and resid 65 through 75 removed outlier: 5.201A pdb=" N HIS L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 102 removed outlier: 3.712A pdb=" N PHE L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR L 95 " --> pdb=" O ILE L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 121 Processing helix chain 'L' and resid 123 through 138 removed outlier: 3.615A pdb=" N GLY L 138 " --> pdb=" O ARG L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 1409 through 1411 No H-bonds generated for 'chain 'M' and resid 1409 through 1411' Processing helix chain 'M' and resid 1437 through 1441 Processing helix chain 'M' and resid 1452 through 1461 removed outlier: 3.878A pdb=" N GLN M1460 " --> pdb=" O GLY M1456 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN M1461 " --> pdb=" O LYS M1457 " (cutoff:3.500A) Processing helix chain 'M' and resid 1525 through 1546 removed outlier: 4.328A pdb=" N MET M1535 " --> pdb=" O ILE M1531 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS M1538 " --> pdb=" O GLN M1534 " (cutoff:3.500A) Processing helix chain 'M' and resid 1566 through 1569 No H-bonds generated for 'chain 'M' and resid 1566 through 1569' Processing helix chain 'M' and resid 1571 through 1583 Processing helix chain 'M' and resid 1597 through 1602 removed outlier: 3.576A pdb=" N GLY M1602 " --> pdb=" O LYS M1599 " (cutoff:3.500A) Processing helix chain 'M' and resid 1604 through 1608 Processing helix chain 'M' and resid 1629 through 1641 removed outlier: 3.868A pdb=" N LYS M1633 " --> pdb=" O PRO M1629 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS M1634 " --> pdb=" O THR M1630 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU M1635 " --> pdb=" O LEU M1631 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL M1636 " --> pdb=" O LEU M1632 " (cutoff:3.500A) Processing helix chain 'M' and resid 1645 through 1655 Processing helix chain 'M' and resid 1667 through 1682 Processing helix chain 'M' and resid 1701 through 1703 No H-bonds generated for 'chain 'M' and resid 1701 through 1703' Processing helix chain 'M' and resid 1707 through 1713 Processing helix chain 'M' and resid 1739 through 1748 removed outlier: 4.855A pdb=" N ALA M1748 " --> pdb=" O ILE M1744 " (cutoff:3.500A) Processing helix chain 'M' and resid 1785 through 1803 Processing helix chain 'M' and resid 1807 through 1819 Processing helix chain 'M' and resid 1830 through 1854 Processing helix chain 'M' and resid 1879 through 1891 Processing helix chain 'M' and resid 1893 through 1895 No H-bonds generated for 'chain 'M' and resid 1893 through 1895' Processing helix chain 'M' and resid 1940 through 1944 Processing helix chain 'M' and resid 1947 through 1975 Proline residue: M1951 - end of helix Processing helix chain 'M' and resid 2003 through 2025 removed outlier: 4.282A pdb=" N PHE M2007 " --> pdb=" O PHE M2003 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LYS M2009 " --> pdb=" O HIS M2005 " (cutoff:3.500A) Proline residue: M2010 - end of helix Processing helix chain 'M' and resid 2050 through 2063 Processing helix chain 'M' and resid 2069 through 2082 removed outlier: 3.714A pdb=" N ILE M2082 " --> pdb=" O GLU M2078 " (cutoff:3.500A) Processing helix chain 'M' and resid 2124 through 2126 No H-bonds generated for 'chain 'M' and resid 2124 through 2126' Processing helix chain 'M' and resid 2139 through 2158 Processing helix chain 'M' and resid 2191 through 2208 Processing helix chain 'M' and resid 2211 through 2220 Processing helix chain 'N' and resid 14 through 28 Proline residue: N 19 - end of helix removed outlier: 3.701A pdb=" N ARG N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 48 Processing helix chain 'N' and resid 56 through 69 Processing helix chain 'N' and resid 80 through 95 Processing helix chain 'N' and resid 166 through 168 No H-bonds generated for 'chain 'N' and resid 166 through 168' Processing helix chain 'N' and resid 211 through 236 removed outlier: 4.693A pdb=" N PHE N 218 " --> pdb=" O LYS N 214 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU N 219 " --> pdb=" O VAL N 215 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG N 221 " --> pdb=" O MET N 217 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN N 234 " --> pdb=" O MET N 230 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE N 235 " --> pdb=" O ARG N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 274 Processing helix chain 'N' and resid 352 through 359 removed outlier: 3.601A pdb=" N THR N 358 " --> pdb=" O ILE N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 381 through 393 Processing helix chain 'N' and resid 411 through 426 removed outlier: 3.724A pdb=" N ASP N 426 " --> pdb=" O GLN N 422 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 470 removed outlier: 3.521A pdb=" N PHE N 458 " --> pdb=" O SER N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 493 through 496 No H-bonds generated for 'chain 'N' and resid 493 through 496' Processing helix chain 'N' and resid 510 through 512 No H-bonds generated for 'chain 'N' and resid 510 through 512' Processing helix chain 'N' and resid 514 through 519 Processing helix chain 'N' and resid 546 through 553 Processing helix chain 'N' and resid 595 through 609 Processing sheet with id= A, first strand: chain '2' and resid 241 through 245 removed outlier: 6.731A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL 2 244 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG 2 296 " --> pdb=" O VAL 2 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 405 through 410 removed outlier: 3.843A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN 2 391 " --> pdb=" O VAL 2 324 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL 2 324 " --> pdb=" O GLN 2 391 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 331 through 334 Processing sheet with id= D, first strand: chain '2' and resid 339 through 341 removed outlier: 4.274A pdb=" N ARG 2 374 " --> pdb=" O ASN 2 340 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 679 through 683 removed outlier: 4.149A pdb=" N GLY 2 543 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 578 through 582 Processing sheet with id= G, first strand: chain '2' and resid 630 through 633 Processing sheet with id= H, first strand: chain '3' and resid 95 through 99 removed outlier: 7.046A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER 3 156 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain '3' and resid 165 through 167 removed outlier: 8.001A pdb=" N LEU 3 166 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N SER 3 181 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 208 through 213 removed outlier: 4.125A pdb=" N ARG 3 208 " --> pdb=" O ALA 3 203 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 273 through 276 removed outlier: 3.784A pdb=" N LYS 3 188 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN 3 259 " --> pdb=" O VAL 3 186 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 259 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '3' and resid 545 through 549 Processing sheet with id= M, first strand: chain '3' and resid 444 through 448 Processing sheet with id= N, first strand: chain '3' and resid 494 through 499 removed outlier: 3.510A pdb=" N LYS 3 499 " --> pdb=" O ILE 3 502 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '3' and resid 195 through 198 removed outlier: 6.621A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '4' and resid 414 through 417 removed outlier: 4.082A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS 4 324 " --> pdb=" O PHE 4 439 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 347 through 349 Processing sheet with id= R, first strand: chain '4' and resid 704 through 706 removed outlier: 3.661A pdb=" N LEU 4 672 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '4' and resid 604 through 607 removed outlier: 3.714A pdb=" N GLU 4 617 " --> pdb=" O TYR 4 604 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '4' and resid 653 through 658 Processing sheet with id= U, first strand: chain '4' and resid 916 through 918 Processing sheet with id= V, first strand: chain '4' and resid 339 through 344 removed outlier: 6.750A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '5' and resid 60 through 64 removed outlier: 6.626A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain '5' and resid 159 through 165 removed outlier: 9.407A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE 5 330 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER 5 168 " --> pdb=" O LYS 5 257 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN 5 259 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE 5 166 " --> pdb=" O GLN 5 259 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 189 through 193 Processing sheet with id= Z, first strand: chain '5' and resid 552 through 556 Processing sheet with id= AA, first strand: chain '5' and resid 451 through 455 Processing sheet with id= AB, first strand: chain '5' and resid 501 through 506 Processing sheet with id= AC, first strand: chain '5' and resid 727 through 729 Processing sheet with id= AD, first strand: chain '5' and resid 173 through 178 removed outlier: 6.512A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '6' and resid 150 through 154 removed outlier: 7.344A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain '6' and resid 394 through 396 removed outlier: 6.603A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR 6 450 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 11.740A pdb=" N ASP 6 378 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE 6 452 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ILE 6 380 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 380 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ARG 6 382 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA 6 456 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 344 through 346 removed outlier: 6.522A pdb=" N PHE 6 309 " --> pdb=" O ASP 6 319 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP 6 319 " --> pdb=" O PHE 6 309 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS 6 311 " --> pdb=" O ILE 6 317 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE 6 317 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '6' and resid 571 through 575 removed outlier: 6.711A pdb=" N LEU 6 711 " --> pdb=" O CYS 6 572 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL 6 574 " --> pdb=" O LEU 6 711 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE 6 713 " --> pdb=" O VAL 6 574 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain '6' and resid 595 through 599 removed outlier: 6.586A pdb=" N ILE 6 635 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR 6 598 " --> pdb=" O ILE 6 635 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS 6 637 " --> pdb=" O THR 6 598 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain '6' and resid 610 through 614 Processing sheet with id= AK, first strand: chain '6' and resid 660 through 664 Processing sheet with id= AL, first strand: chain '6' and resid 301 through 306 removed outlier: 6.783A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 77 through 81 removed outlier: 6.712A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain '7' and resid 238 through 244 removed outlier: 3.581A pdb=" N ARG 7 382 " --> pdb=" O ASP 7 350 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 268 through 272 removed outlier: 7.045A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '7' and resid 456 through 458 removed outlier: 7.278A pdb=" N ILE 7 596 " --> pdb=" O CYS 7 457 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain '7' and resid 481 through 484 removed outlier: 6.562A pdb=" N SER 7 562 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE 7 523 " --> pdb=" O SER 7 562 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU 7 564 " --> pdb=" O ILE 7 523 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '7' and resid 545 through 547 Processing sheet with id= AS, first strand: chain 'A' and resid 162 through 166 Processing sheet with id= AT, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.878A pdb=" N GLY A 172 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 24 through 28 Processing sheet with id= AV, first strand: chain 'C' and resid 43 through 47 Processing sheet with id= AW, first strand: chain 'D' and resid 274 through 278 Processing sheet with id= AX, first strand: chain 'D' and resid 255 through 260 Processing sheet with id= AY, first strand: chain 'E' and resid 56 through 61 removed outlier: 6.975A pdb=" N LEU E 27 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL E 59 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER E 80 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE E 30 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU E 82 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER E 32 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL E 84 " --> pdb=" O SER E 32 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'E' and resid 316 through 322 Processing sheet with id= BA, first strand: chain 'E' and resid 525 through 530 removed outlier: 7.897A pdb=" N CYS E 528 " --> pdb=" O PRO E 566 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL E 568 " --> pdb=" O CYS E 528 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU E 530 " --> pdb=" O VAL E 568 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA E 570 " --> pdb=" O LEU E 530 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'E' and resid 578 through 581 Processing sheet with id= BC, first strand: chain 'F' and resid 526 through 529 removed outlier: 3.548A pdb=" N VAL F 505 " --> pdb=" O SER F 512 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR F 495 " --> pdb=" O VAL F 502 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR F 504 " --> pdb=" O TYR F 493 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR F 493 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'F' and resid 536 through 539 Processing sheet with id= BE, first strand: chain 'F' and resid 581 through 583 Processing sheet with id= BF, first strand: chain 'F' and resid 637 through 642 removed outlier: 3.611A pdb=" N VAL F 628 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA F 617 " --> pdb=" O VAL F 628 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'F' and resid 705 through 707 Processing sheet with id= BH, first strand: chain 'F' and resid 740 through 748 removed outlier: 6.756A pdb=" N ASN F 753 " --> pdb=" O LEU F 745 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU F 747 " --> pdb=" O THR F 751 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR F 751 " --> pdb=" O LEU F 747 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 511 through 516 removed outlier: 3.873A pdb=" N THR G 495 " --> pdb=" O VAL G 502 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR G 504 " --> pdb=" O TYR G 493 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TYR G 493 " --> pdb=" O THR G 504 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'G' and resid 536 through 539 removed outlier: 3.521A pdb=" N GLY G 547 " --> pdb=" O LEU G 536 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'G' and resid 581 through 583 Processing sheet with id= BL, first strand: chain 'G' and resid 615 through 620 removed outlier: 7.164A pdb=" N VAL G 628 " --> pdb=" O VAL G 616 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU G 618 " --> pdb=" O PHE G 626 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE G 626 " --> pdb=" O LEU G 618 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS G 652 " --> pdb=" O LEU G 640 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU G 642 " --> pdb=" O TYR G 650 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR G 650 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'G' and resid 742 through 744 Processing sheet with id= BN, first strand: chain 'H' and resid 526 through 530 removed outlier: 3.588A pdb=" N VAL H 515 " --> pdb=" O TYR H 526 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE H 528 " --> pdb=" O ILE H 513 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE H 513 " --> pdb=" O PHE H 528 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR H 511 " --> pdb=" O ASP H 530 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR H 495 " --> pdb=" O VAL H 502 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR H 504 " --> pdb=" O TYR H 493 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR H 493 " --> pdb=" O THR H 504 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'H' and resid 536 through 540 removed outlier: 3.601A pdb=" N GLY H 543 " --> pdb=" O ASN H 540 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'H' and resid 553 through 556 removed outlier: 3.784A pdb=" N TYR H 556 " --> pdb=" O TRP H 566 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TRP H 566 " --> pdb=" O TYR H 556 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'H' and resid 581 through 583 Processing sheet with id= BR, first strand: chain 'H' and resid 615 through 620 removed outlier: 3.576A pdb=" N VAL H 616 " --> pdb=" O VAL H 628 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL H 628 " --> pdb=" O VAL H 616 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU H 618 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE H 626 " --> pdb=" O LEU H 618 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA H 620 " --> pdb=" O ARG H 624 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG H 624 " --> pdb=" O ALA H 620 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU H 642 " --> pdb=" O TYR H 650 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR H 650 " --> pdb=" O GLU H 642 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'H' and resid 772 through 774 removed outlier: 3.867A pdb=" N ALA H 746 " --> pdb=" O ASN H 753 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE H 755 " --> pdb=" O PRO H 744 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'K' and resid 363 through 368 removed outlier: 3.510A pdb=" N LEU K 364 " --> pdb=" O VAL K 376 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU K 374 " --> pdb=" O ILE K 366 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR K 368 " --> pdb=" O THR K 372 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'M' and resid 1337 through 1341 removed outlier: 3.590A pdb=" N VAL M1340 " --> pdb=" O GLN M1347 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'M' and resid 1508 through 1511 removed outlier: 6.057A pdb=" N ASN M1557 " --> pdb=" O ILE M1509 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE M1511 " --> pdb=" O ASN M1557 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLU M1559 " --> pdb=" O ILE M1511 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'M' and resid 1590 through 1592 Processing sheet with id= BX, first strand: chain 'M' and resid 1899 through 1902 removed outlier: 3.812A pdb=" N ASP M1899 " --> pdb=" O ASP M1737 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN M1901 " --> pdb=" O GLY M1735 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR M1860 " --> pdb=" O LEU M1867 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS M1869 " --> pdb=" O ILE M1858 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE M1858 " --> pdb=" O LYS M1869 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'M' and resid 1934 through 1939 removed outlier: 3.675A pdb=" N LEU M1908 " --> pdb=" O LEU M1920 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'M' and resid 2162 through 2164 Processing sheet with id= CA, first strand: chain 'N' and resid 325 through 331 removed outlier: 5.071A pdb=" N TRP N 296 " --> pdb=" O ILE N 307 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL N 341 " --> pdb=" O ASP N 308 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU N 329 " --> pdb=" O THR N 342 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET N 344 " --> pdb=" O LEU N 327 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU N 327 " --> pdb=" O MET N 344 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'N' and resid 681 through 684 removed outlier: 6.120A pdb=" N LEU N 431 " --> pdb=" O VAL N 400 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR N 480 " --> pdb=" O LEU N 432 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N TRP N 434 " --> pdb=" O THR N 480 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE N 482 " --> pdb=" O TRP N 434 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'N' and resid 530 through 532 removed outlier: 6.756A pdb=" N THR N 638 " --> pdb=" O VAL N 540 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N PHE N 542 " --> pdb=" O THR N 638 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL N 640 " --> pdb=" O PHE N 542 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS N 657 " --> pdb=" O MET N 639 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU N 641 " --> pdb=" O LYS N 657 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE N 659 " --> pdb=" O LEU N 641 " (cutoff:3.500A) 2552 hydrogen bonds defined for protein. 7479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.23 Time building geometry restraints manager: 24.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 22995 1.35 - 1.50: 18980 1.50 - 1.65: 29549 1.65 - 1.80: 295 1.80 - 1.95: 208 Bond restraints: 72027 Sorted by residual: bond pdb=" N CYS 4 567 " pdb=" CA CYS 4 567 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.58e+01 bond pdb=" C ASP M1810 " pdb=" O ASP M1810 " ideal model delta sigma weight residual 1.237 1.289 -0.052 1.17e-02 7.31e+03 1.98e+01 bond pdb=" C ASN M1814 " pdb=" O ASN M1814 " ideal model delta sigma weight residual 1.237 1.286 -0.049 1.17e-02 7.31e+03 1.78e+01 bond pdb=" N LEU K 414 " pdb=" CA LEU K 414 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.71e+01 bond pdb=" C GLN A 18 " pdb=" O GLN A 18 " ideal model delta sigma weight residual 1.237 1.280 -0.043 1.17e-02 7.31e+03 1.35e+01 ... (remaining 72022 not shown) Histogram of bond angle deviations from ideal: 98.00 - 105.55: 1546 105.55 - 113.09: 39999 113.09 - 120.64: 31343 120.64 - 128.19: 24335 128.19 - 135.74: 449 Bond angle restraints: 97672 Sorted by residual: angle pdb=" N LEU B 160 " pdb=" CA LEU B 160 " pdb=" C LEU B 160 " ideal model delta sigma weight residual 113.19 104.38 8.81 1.19e+00 7.06e-01 5.48e+01 angle pdb=" N LYS 7 364 " pdb=" CA LYS 7 364 " pdb=" C LYS 7 364 " ideal model delta sigma weight residual 112.87 105.17 7.70 1.20e+00 6.94e-01 4.12e+01 angle pdb=" C ASP M1810 " pdb=" N LEU M1811 " pdb=" CA LEU M1811 " ideal model delta sigma weight residual 120.54 112.86 7.68 1.35e+00 5.49e-01 3.24e+01 angle pdb=" C CYS 4 567 " pdb=" CA CYS 4 567 " pdb=" CB CYS 4 567 " ideal model delta sigma weight residual 117.07 109.28 7.79 1.44e+00 4.82e-01 2.93e+01 angle pdb=" C TYR 2 194 " pdb=" N SER 2 195 " pdb=" CA SER 2 195 " ideal model delta sigma weight residual 120.38 113.56 6.82 1.37e+00 5.33e-01 2.48e+01 ... (remaining 97667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.73: 42346 33.73 - 67.46: 1345 67.46 - 101.19: 89 101.19 - 134.92: 2 134.92 - 168.65: 4 Dihedral angle restraints: 43786 sinusoidal: 18253 harmonic: 25533 Sorted by residual: dihedral pdb=" C5' ADP 31001 " pdb=" O5' ADP 31001 " pdb=" PA ADP 31001 " pdb=" O2A ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 108.65 -168.65 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PA ADP 31001 " pdb=" PB ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 97.90 -157.90 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" O1B ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PB ADP 31001 " pdb=" PA ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 74.94 -134.95 1 2.00e+01 2.50e-03 4.10e+01 ... (remaining 43783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 8594 0.047 - 0.094: 1960 0.094 - 0.140: 524 0.140 - 0.187: 60 0.187 - 0.234: 18 Chirality restraints: 11156 Sorted by residual: chirality pdb=" CA VAL 4 771 " pdb=" N VAL 4 771 " pdb=" C VAL 4 771 " pdb=" CB VAL 4 771 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE 5 333 " pdb=" N ILE 5 333 " pdb=" C ILE 5 333 " pdb=" CB ILE 5 333 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU M1816 " pdb=" N LEU M1816 " pdb=" C LEU M1816 " pdb=" CB LEU M1816 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 11153 not shown) Planarity restraints: 12268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 4 790 " -0.748 9.50e-02 1.11e+02 3.36e-01 6.85e+01 pdb=" NE ARG 4 790 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG 4 790 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG 4 790 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 4 790 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 159 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C GLY B 159 " 0.074 2.00e-02 2.50e+03 pdb=" O GLY B 159 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 160 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER 3 300 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C SER 3 300 " -0.066 2.00e-02 2.50e+03 pdb=" O SER 3 300 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU 3 301 " 0.022 2.00e-02 2.50e+03 ... (remaining 12265 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 609 2.54 - 3.13: 56451 3.13 - 3.72: 112917 3.72 - 4.31: 154483 4.31 - 4.90: 258107 Nonbonded interactions: 582567 Sorted by model distance: nonbonded pdb=" O3G AGS 5 802 " pdb="MG MG 5 803 " model vdw 1.954 2.170 nonbonded pdb=" OG SER 5 423 " pdb="MG MG 5 803 " model vdw 1.973 2.170 nonbonded pdb=" O2B ADP 31001 " pdb="MG MG 31002 " model vdw 2.017 2.170 nonbonded pdb="MG MG 61102 " pdb=" O1B AGS 61103 " model vdw 2.044 2.170 nonbonded pdb=" OG SER 6 582 " pdb="MG MG 61102 " model vdw 2.048 2.170 ... (remaining 582562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and (resid 474 through 490 or (resid 491 and (name N or name CA or na \ me C or name O or name CB )) or resid 492 through 576 or (resid 577 and (name N \ or name CA or name C or name O or name CB )) or resid 578 through 586 or (resid \ 587 and (name N or name CA or name C or name O or name CB )) or resid 588 throug \ h 665 or resid 670 through 782 or (resid 783 and (name N or name CA or name C or \ name O or name CB )) or resid 784 or resid 816 through 889 or (resid 890 and (n \ ame N or name CA or name C or name O or name CB )) or resid 891 through 899 or ( \ resid 900 and (name N or name CA or name C or name O or name CB )) or resid 901 \ or (resid 902 and (name N or name CA or name C or name O or name CB )) or resid \ 903 through 922)) selection = (chain 'G' and (resid 474 through 490 or (resid 491 and (name N or name CA or na \ me C or name O or name CB )) or resid 492 through 586 or (resid 587 and (name N \ or name CA or name C or name O or name CB )) or resid 588 through 665 or resid 6 \ 70 through 782 or (resid 783 and (name N or name CA or name C or name O or name \ CB )) or resid 784 or resid 816 through 901 or (resid 902 and (name N or name CA \ or name C or name O or name CB )) or resid 903 through 909 or (resid 910 and (n \ ame N or name CA or name C or name O or name CB )) or resid 911 through 922)) selection = (chain 'H' and (resid 474 through 576 or (resid 577 and (name N or name CA or na \ me C or name O or name CB )) or resid 578 through 784 or resid 816 through 889 o \ r (resid 890 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 91 through 899 or (resid 900 and (name N or name CA or name C or name O or name \ CB )) or resid 901 through 909 or (resid 910 and (name N or name CA or name C or \ name O or name CB )) or resid 911 through 922)) } 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: 9.160 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: 0.050 Extract box with map and model: 32.870 Check model and map are aligned: 0.800 Set scattering table: 0.520 Process input model: 157.900 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.004 0.052 72027 Z= 0.281 Angle : 0.587 9.537 97672 Z= 0.348 Chirality : 0.044 0.234 11156 Planarity : 0.005 0.336 12268 Dihedral : 15.738 168.649 27190 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.09 % Favored : 94.75 % Rotamer: Outliers : 1.30 % Allowed : 0.80 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 8553 helix: 1.19 (0.09), residues: 3614 sheet: -1.00 (0.15), residues: 1274 loop : -0.78 (0.11), residues: 3665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP E 473 HIS 0.004 0.001 HIS 6 669 PHE 0.029 0.001 PHE 7 355 TYR 0.021 0.001 TYR E 2 ARG 0.016 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 339 time to evaluate : 6.245 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: 2 501 MET cc_start: 0.8957 (mmt) cc_final: 0.8498 (mmt) REVERT: 3 280 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: 4 777 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7906 (mtp) REVERT: 4 792 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8025 (p) REVERT: 4 874 LYS cc_start: 0.4528 (OUTLIER) cc_final: 0.3534 (mmtt) REVERT: 7 402 MET cc_start: 0.8263 (tpt) cc_final: 0.8052 (tpp) REVERT: 7 541 MET cc_start: 0.8078 (ttt) cc_final: 0.7874 (ttp) REVERT: A 20 TYR cc_start: 0.7564 (t80) cc_final: 0.7327 (t80) REVERT: A 100 MET cc_start: 0.8387 (mtp) cc_final: 0.8046 (mtp) REVERT: B 63 MET cc_start: 0.9278 (mtm) cc_final: 0.8857 (mtp) REVERT: F 778 MET cc_start: 0.4680 (mmt) cc_final: 0.4028 (mmm) REVERT: G 726 MET cc_start: 0.3043 (ttt) cc_final: 0.2750 (ttp) REVERT: H 477 MET cc_start: 0.6543 (mpp) cc_final: 0.6313 (mpp) REVERT: M 1805 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: M 2107 LEU cc_start: 0.9019 (tt) cc_final: 0.8668 (tp) REVERT: N 91 MET cc_start: 0.6836 (ppp) cc_final: 0.6599 (ppp) outliers start: 100 outliers final: 37 residues processed: 430 average time/residue: 0.6635 time to fit residues: 491.9550 Evaluate side-chains 331 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 289 time to evaluate : 6.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 3 residue 280 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 4 residue 574 LYS Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 772 ARG Chi-restraints excluded: chain 4 residue 777 MET Chi-restraints excluded: chain 4 residue 782 ASP Chi-restraints excluded: chain 4 residue 792 THR Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 4 residue 869 ILE Chi-restraints excluded: chain 4 residue 874 LYS Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 341 SER Chi-restraints excluded: chain 6 residue 737 LYS Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 555 GLN Chi-restraints excluded: chain H residue 557 ARG Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 631 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain M residue 1411 LYS Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1583 GLU Chi-restraints excluded: chain M residue 1797 GLU Chi-restraints excluded: chain M residue 1800 ASP Chi-restraints excluded: chain M residue 1805 GLU Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1812 LEU Chi-restraints excluded: chain M residue 1815 SER Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1819 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 732 optimal weight: 5.9990 chunk 657 optimal weight: 20.0000 chunk 365 optimal weight: 6.9990 chunk 224 optimal weight: 0.5980 chunk 443 optimal weight: 6.9990 chunk 351 optimal weight: 0.9980 chunk 680 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 413 optimal weight: 0.6980 chunk 506 optimal weight: 3.9990 chunk 788 optimal weight: 6.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 GLN 3 310 ASN ** 3 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 576 GLN ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 652 GLN 4 871 ASN ** 5 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 335 ASN ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 ASN A 71 GLN C 136 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN E 550 ASN E 624 ASN ** F 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 680 ASN ** H 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 72027 Z= 0.387 Angle : 0.557 13.100 97672 Z= 0.285 Chirality : 0.042 0.208 11156 Planarity : 0.004 0.060 12268 Dihedral : 10.589 175.867 10211 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.79 % Allowed : 6.51 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 8553 helix: 1.21 (0.09), residues: 3622 sheet: -1.04 (0.15), residues: 1300 loop : -0.79 (0.11), residues: 3631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 718 HIS 0.005 0.001 HIS 2 868 PHE 0.028 0.001 PHE 2 271 TYR 0.025 0.001 TYR F 862 ARG 0.006 0.000 ARG 4 796 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 292 time to evaluate : 6.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 501 MET cc_start: 0.8898 (mmt) cc_final: 0.8462 (mmt) REVERT: 7 506 MET cc_start: 0.5788 (ppp) cc_final: 0.5166 (ppp) REVERT: A 100 MET cc_start: 0.8443 (mtp) cc_final: 0.8078 (mtp) REVERT: B 63 MET cc_start: 0.9384 (mtm) cc_final: 0.9164 (mtp) REVERT: F 726 MET cc_start: 0.8640 (tpp) cc_final: 0.8408 (tpt) REVERT: F 778 MET cc_start: 0.4449 (mmt) cc_final: 0.3947 (mmm) REVERT: H 477 MET cc_start: 0.5961 (mpp) cc_final: 0.5551 (mpp) REVERT: M 2107 LEU cc_start: 0.9077 (tt) cc_final: 0.8800 (tp) outliers start: 61 outliers final: 44 residues processed: 342 average time/residue: 0.6383 time to fit residues: 384.5573 Evaluate side-chains 322 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 278 time to evaluate : 6.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 772 ARG Chi-restraints excluded: chain 4 residue 792 THR Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 4 residue 869 ILE Chi-restraints excluded: chain 5 residue 21 ASP Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 341 SER Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 418 LEU Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1805 GLU Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1812 LEU Chi-restraints excluded: chain M residue 1815 SER Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 438 optimal weight: 0.0970 chunk 244 optimal weight: 5.9990 chunk 656 optimal weight: 4.9990 chunk 536 optimal weight: 9.9990 chunk 217 optimal weight: 0.5980 chunk 789 optimal weight: 4.9990 chunk 853 optimal weight: 2.9990 chunk 703 optimal weight: 7.9990 chunk 783 optimal weight: 0.9990 chunk 269 optimal weight: 0.9990 chunk 633 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 391 GLN ** 3 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN F 916 ASN ** H 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 575 ASN ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1806 ASN M1838 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 72027 Z= 0.206 Angle : 0.476 9.074 97672 Z= 0.246 Chirality : 0.040 0.176 11156 Planarity : 0.003 0.060 12268 Dihedral : 10.267 174.165 10161 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.88 % Allowed : 9.20 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.09), residues: 8553 helix: 1.36 (0.09), residues: 3617 sheet: -1.06 (0.15), residues: 1296 loop : -0.71 (0.11), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 473 HIS 0.004 0.001 HIS 7 538 PHE 0.021 0.001 PHE 2 271 TYR 0.021 0.001 TYR 5 730 ARG 0.008 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 288 time to evaluate : 6.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 261 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8202 (mmt) REVERT: 7 506 MET cc_start: 0.5479 (ppp) cc_final: 0.5046 (ppp) REVERT: 7 600 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8352 (ptp) REVERT: A 14 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8805 (ttmm) REVERT: B 63 MET cc_start: 0.9366 (mtm) cc_final: 0.8968 (mtp) REVERT: C 36 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7206 (tpt170) REVERT: F 726 MET cc_start: 0.8718 (tpp) cc_final: 0.8457 (tpt) REVERT: F 778 MET cc_start: 0.4249 (mmt) cc_final: 0.3808 (mmm) REVERT: M 2107 LEU cc_start: 0.9096 (tt) cc_final: 0.8833 (tp) outliers start: 68 outliers final: 44 residues processed: 340 average time/residue: 0.6394 time to fit residues: 383.9534 Evaluate side-chains 325 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 277 time to evaluate : 6.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 2 residue 489 ARG Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 792 THR Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 21 ASP Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 668 ILE Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1805 GLU Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1812 LEU Chi-restraints excluded: chain M residue 1815 SER Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain N residue 91 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 780 optimal weight: 3.9990 chunk 593 optimal weight: 0.0030 chunk 409 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 376 optimal weight: 1.9990 chunk 530 optimal weight: 0.9980 chunk 792 optimal weight: 3.9990 chunk 839 optimal weight: 6.9990 chunk 414 optimal weight: 1.9990 chunk 751 optimal weight: 30.0000 chunk 226 optimal weight: 0.9980 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 391 GLN ** 3 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 646 HIS ** 5 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN H 601 ASN ** H 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 575 ASN ** M1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 72027 Z= 0.180 Angle : 0.461 7.961 97672 Z= 0.237 Chirality : 0.039 0.166 11156 Planarity : 0.003 0.060 12268 Dihedral : 10.108 166.014 10148 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.03 % Allowed : 10.78 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 8553 helix: 1.46 (0.09), residues: 3622 sheet: -1.02 (0.15), residues: 1301 loop : -0.67 (0.11), residues: 3630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 473 HIS 0.003 0.001 HIS 7 538 PHE 0.016 0.001 PHE 2 271 TYR 0.019 0.001 TYR F 862 ARG 0.010 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 294 time to evaluate : 6.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 184 GLU cc_start: 0.8299 (tp30) cc_final: 0.8091 (mm-30) REVERT: 6 726 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: 7 433 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8224 (mt) REVERT: 7 506 MET cc_start: 0.5530 (ppp) cc_final: 0.5076 (ppp) REVERT: 7 542 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: 7 600 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8213 (ptp) REVERT: A 14 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8791 (ttmm) REVERT: B 63 MET cc_start: 0.9333 (mtm) cc_final: 0.8804 (mtp) REVERT: F 668 MET cc_start: 0.6052 (ptm) cc_final: 0.5822 (pmm) REVERT: F 726 MET cc_start: 0.8725 (tpp) cc_final: 0.8454 (tpt) REVERT: F 778 MET cc_start: 0.4324 (mmt) cc_final: 0.3879 (mmm) REVERT: M 1322 TRP cc_start: 0.6439 (p90) cc_final: 0.6232 (p90) REVERT: M 2107 LEU cc_start: 0.9076 (tt) cc_final: 0.8816 (tp) outliers start: 79 outliers final: 44 residues processed: 359 average time/residue: 0.6348 time to fit residues: 406.9948 Evaluate side-chains 333 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 284 time to evaluate : 6.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 21 ASP Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 511 ASP Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 433 LEU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 566 SER Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1815 SER Chi-restraints excluded: chain M residue 1838 ASN Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 698 optimal weight: 30.0000 chunk 476 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 624 optimal weight: 30.0000 chunk 346 optimal weight: 0.8980 chunk 715 optimal weight: 0.8980 chunk 579 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 428 optimal weight: 0.8980 chunk 753 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 391 GLN ** 3 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN E 550 ASN E 624 ASN ** H 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 HIS K 575 ASN ** M1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 72027 Z= 0.255 Angle : 0.479 7.521 97672 Z= 0.246 Chirality : 0.040 0.179 11156 Planarity : 0.003 0.059 12268 Dihedral : 10.075 161.899 10141 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.06 % Allowed : 11.73 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 8553 helix: 1.47 (0.09), residues: 3619 sheet: -1.02 (0.15), residues: 1289 loop : -0.69 (0.11), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 473 HIS 0.004 0.001 HIS M1837 PHE 0.019 0.001 PHE 2 271 TYR 0.018 0.001 TYR F 862 ARG 0.010 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 285 time to evaluate : 6.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 726 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: 7 257 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8636 (p) REVERT: 7 433 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8174 (mt) REVERT: 7 506 MET cc_start: 0.5513 (ppp) cc_final: 0.5073 (ppp) REVERT: 7 542 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: 7 600 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8212 (ptp) REVERT: A 14 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8783 (ttmm) REVERT: B 63 MET cc_start: 0.9384 (mtm) cc_final: 0.8862 (mtp) REVERT: F 726 MET cc_start: 0.8745 (tpp) cc_final: 0.8461 (tpt) REVERT: F 778 MET cc_start: 0.4313 (mmt) cc_final: 0.3872 (mmm) REVERT: H 659 MET cc_start: 0.5949 (tmm) cc_final: 0.5704 (tmm) REVERT: M 1322 TRP cc_start: 0.6402 (p90) cc_final: 0.6134 (p90) outliers start: 82 outliers final: 58 residues processed: 353 average time/residue: 0.6276 time to fit residues: 394.7094 Evaluate side-chains 343 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 279 time to evaluate : 6.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 481 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 21 ASP Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 511 ASP Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 433 LEU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 566 SER Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 0.7980 chunk 755 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 492 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 839 optimal weight: 3.9990 chunk 697 optimal weight: 40.0000 chunk 388 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 440 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 GLN ** 2 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 210 ASN 7 412 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN E 550 ASN E 596 HIS E 624 ASN M1821 GLN M1838 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 72027 Z= 0.401 Angle : 0.542 12.130 97672 Z= 0.277 Chirality : 0.042 0.209 11156 Planarity : 0.004 0.059 12268 Dihedral : 10.174 159.342 10136 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.38 % Allowed : 12.38 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.09), residues: 8553 helix: 1.33 (0.09), residues: 3621 sheet: -1.10 (0.15), residues: 1300 loop : -0.77 (0.11), residues: 3632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 473 HIS 0.005 0.001 HIS 5 155 PHE 0.029 0.001 PHE 2 271 TYR 0.022 0.001 TYR 5 46 ARG 0.012 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 274 time to evaluate : 6.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 347 THR cc_start: 0.7255 (OUTLIER) cc_final: 0.7053 (p) REVERT: 6 726 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: 7 257 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8655 (p) REVERT: 7 433 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8195 (mt) REVERT: 7 506 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5382 (ppp) REVERT: 7 542 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: 7 600 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8267 (ptp) REVERT: A 14 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8848 (ttmm) REVERT: B 63 MET cc_start: 0.9409 (mtm) cc_final: 0.8999 (mtp) REVERT: B 144 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8673 (mttm) REVERT: E 362 MET cc_start: 0.9246 (tmm) cc_final: 0.8897 (ttt) REVERT: F 726 MET cc_start: 0.8762 (tpp) cc_final: 0.8456 (tpt) REVERT: F 778 MET cc_start: 0.4290 (mmt) cc_final: 0.3865 (mmm) REVERT: G 778 MET cc_start: 0.2502 (mmt) cc_final: 0.0502 (mmt) REVERT: H 659 MET cc_start: 0.6000 (tmm) cc_final: 0.5739 (tmm) REVERT: M 1322 TRP cc_start: 0.6502 (p90) cc_final: 0.6251 (p90) outliers start: 106 outliers final: 68 residues processed: 364 average time/residue: 0.6266 time to fit residues: 410.3118 Evaluate side-chains 352 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 275 time to evaluate : 6.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 2 residue 303 ILE Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 481 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 652 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 533 LEU Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 511 ASP Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 433 LEU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 506 MET Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 757 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 420 ASN Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 566 SER Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 91 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 478 optimal weight: 3.9990 chunk 613 optimal weight: 6.9990 chunk 475 optimal weight: 0.9980 chunk 706 optimal weight: 40.0000 chunk 468 optimal weight: 0.9990 chunk 836 optimal weight: 3.9990 chunk 523 optimal weight: 1.9990 chunk 510 optimal weight: 0.7980 chunk 386 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN E 624 ASN ** M1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 72027 Z= 0.211 Angle : 0.474 12.053 97672 Z= 0.243 Chirality : 0.039 0.182 11156 Planarity : 0.003 0.059 12268 Dihedral : 10.067 152.966 10135 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.10 % Allowed : 13.08 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.09), residues: 8553 helix: 1.43 (0.09), residues: 3626 sheet: -1.05 (0.15), residues: 1286 loop : -0.72 (0.11), residues: 3641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 473 HIS 0.003 0.001 HIS 2 809 PHE 0.014 0.001 PHE 2 271 TYR 0.017 0.001 TYR F 862 ARG 0.008 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 286 time to evaluate : 6.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 749 MET cc_start: 0.8103 (ptp) cc_final: 0.7523 (ptp) REVERT: 6 726 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: 7 433 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8217 (mt) REVERT: 7 506 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.5033 (ppp) REVERT: 7 542 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: 7 600 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8172 (ptp) REVERT: A 14 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8821 (ttmm) REVERT: B 63 MET cc_start: 0.9432 (mtm) cc_final: 0.8937 (mtp) REVERT: B 144 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8625 (mttm) REVERT: F 668 MET cc_start: 0.6244 (ptm) cc_final: 0.5952 (pmm) REVERT: F 726 MET cc_start: 0.8784 (tpp) cc_final: 0.8488 (tpt) REVERT: F 778 MET cc_start: 0.4488 (mmt) cc_final: 0.4107 (mmm) REVERT: G 778 MET cc_start: 0.2247 (mmt) cc_final: 0.0366 (mmt) REVERT: H 477 MET cc_start: 0.5789 (mpp) cc_final: 0.5461 (mpp) REVERT: H 659 MET cc_start: 0.6056 (tmm) cc_final: 0.5797 (tmm) REVERT: M 2107 LEU cc_start: 0.9060 (tt) cc_final: 0.8821 (tp) outliers start: 85 outliers final: 68 residues processed: 356 average time/residue: 0.6469 time to fit residues: 413.8017 Evaluate side-chains 348 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 273 time to evaluate : 6.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 425 THR Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 481 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 652 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 571 SER Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 533 LEU Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 511 ASP Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 433 LEU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 506 MET Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain G residue 723 ASP Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 566 SER Chi-restraints excluded: chain M residue 1432 THR Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 91 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 517 optimal weight: 0.7980 chunk 334 optimal weight: 3.9990 chunk 499 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 531 optimal weight: 0.5980 chunk 569 optimal weight: 6.9990 chunk 413 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 657 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 124 ASN ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 507 ASN ** H 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 537 ASN ** M1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 72027 Z= 0.173 Angle : 0.465 11.837 97672 Z= 0.237 Chirality : 0.039 0.166 11156 Planarity : 0.003 0.059 12268 Dihedral : 9.969 150.532 10135 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.28 % Allowed : 13.18 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.10), residues: 8553 helix: 1.53 (0.09), residues: 3626 sheet: -1.00 (0.15), residues: 1310 loop : -0.68 (0.11), residues: 3617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 473 HIS 0.003 0.000 HIS 7 538 PHE 0.012 0.001 PHE 2 271 TYR 0.017 0.001 TYR 5 730 ARG 0.009 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 283 time to evaluate : 6.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 347 THR cc_start: 0.7113 (OUTLIER) cc_final: 0.6863 (p) REVERT: 6 726 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: 7 433 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8183 (mt) REVERT: 7 506 MET cc_start: 0.5322 (OUTLIER) cc_final: 0.4917 (ppp) REVERT: 7 542 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: 7 600 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8140 (ptp) REVERT: A 1 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7337 (tmm) REVERT: A 14 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8808 (ttmm) REVERT: B 63 MET cc_start: 0.9377 (mtm) cc_final: 0.8830 (mtp) REVERT: B 144 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8595 (mttm) REVERT: F 668 MET cc_start: 0.6251 (ptm) cc_final: 0.5962 (pmm) REVERT: F 726 MET cc_start: 0.8790 (tpp) cc_final: 0.8501 (tpt) REVERT: F 778 MET cc_start: 0.4510 (mmt) cc_final: 0.4114 (mmm) REVERT: G 778 MET cc_start: 0.2187 (mmt) cc_final: 0.0424 (mmt) REVERT: H 477 MET cc_start: 0.5798 (mpp) cc_final: 0.5452 (mpp) REVERT: H 659 MET cc_start: 0.6077 (tmm) cc_final: 0.5803 (tmm) REVERT: K 675 TYR cc_start: 0.4338 (OUTLIER) cc_final: 0.4127 (t80) REVERT: M 1366 MET cc_start: 0.5075 (tpp) cc_final: 0.4502 (mmm) REVERT: M 2107 LEU cc_start: 0.9078 (tt) cc_final: 0.8855 (tp) outliers start: 99 outliers final: 73 residues processed: 368 average time/residue: 0.6164 time to fit residues: 404.7374 Evaluate side-chains 363 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 280 time to evaluate : 6.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 303 ILE Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 20 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 425 THR Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 481 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 652 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 571 SER Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 511 ASP Chi-restraints excluded: chain 6 residue 519 MET Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 433 LEU Chi-restraints excluded: chain 7 residue 435 LEU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 506 MET Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain G residue 723 ASP Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 566 SER Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1432 THR Chi-restraints excluded: chain M residue 1537 GLU Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1838 ASN Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 91 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 761 optimal weight: 20.0000 chunk 801 optimal weight: 3.9990 chunk 731 optimal weight: 20.0000 chunk 779 optimal weight: 7.9990 chunk 469 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 612 optimal weight: 4.9990 chunk 239 optimal weight: 0.9990 chunk 704 optimal weight: 30.0000 chunk 737 optimal weight: 7.9990 chunk 776 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN ** 2 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 730 HIS ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 ASN E 624 ASN ** F 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 72027 Z= 0.419 Angle : 0.559 15.749 97672 Z= 0.283 Chirality : 0.042 0.236 11156 Planarity : 0.004 0.058 12268 Dihedral : 10.124 151.641 10135 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.14 % Allowed : 13.55 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.09), residues: 8553 helix: 1.36 (0.09), residues: 3619 sheet: -1.14 (0.15), residues: 1316 loop : -0.77 (0.11), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 473 HIS 0.013 0.001 HIS M1837 PHE 0.023 0.001 PHE 2 271 TYR 0.023 0.001 TYR 5 46 ARG 0.012 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 273 time to evaluate : 6.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 726 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: 7 433 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8172 (mt) REVERT: 7 506 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.5185 (ppp) REVERT: 7 600 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8233 (ptp) REVERT: A 14 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8857 (ttmm) REVERT: B 63 MET cc_start: 0.9432 (mtm) cc_final: 0.9013 (mtp) REVERT: B 144 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8684 (mttm) REVERT: F 726 MET cc_start: 0.8812 (tpp) cc_final: 0.8515 (tpt) REVERT: F 778 MET cc_start: 0.4472 (mmt) cc_final: 0.4070 (mmm) REVERT: G 778 MET cc_start: 0.2251 (mmt) cc_final: 0.0485 (mmt) REVERT: H 659 MET cc_start: 0.6078 (tmm) cc_final: 0.5858 (tmm) REVERT: K 675 TYR cc_start: 0.4370 (OUTLIER) cc_final: 0.4120 (t80) REVERT: M 1366 MET cc_start: 0.5100 (tpp) cc_final: 0.4454 (mmm) REVERT: M 1438 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7249 (tp) REVERT: M 2107 LEU cc_start: 0.9139 (tt) cc_final: 0.8927 (tp) outliers start: 88 outliers final: 73 residues processed: 348 average time/residue: 0.6282 time to fit residues: 392.1983 Evaluate side-chains 352 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 271 time to evaluate : 6.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 303 ILE Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 20 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 481 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 652 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 571 SER Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 4 residue 916 VAL Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 511 ASP Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 433 LEU Chi-restraints excluded: chain 7 residue 435 LEU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 506 MET Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 725 ASN Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain G residue 723 ASP Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 566 SER Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1432 THR Chi-restraints excluded: chain M residue 1438 ILE Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 511 optimal weight: 0.8980 chunk 824 optimal weight: 20.0000 chunk 503 optimal weight: 0.9990 chunk 391 optimal weight: 2.9990 chunk 573 optimal weight: 0.8980 chunk 864 optimal weight: 6.9990 chunk 795 optimal weight: 0.9990 chunk 688 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 531 optimal weight: 1.9990 chunk 422 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 ASN ** M1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 72027 Z= 0.186 Angle : 0.482 18.021 97672 Z= 0.244 Chirality : 0.039 0.198 11156 Planarity : 0.003 0.059 12268 Dihedral : 10.003 150.487 10135 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.09 % Allowed : 13.74 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 8553 helix: 1.48 (0.09), residues: 3624 sheet: -1.04 (0.15), residues: 1284 loop : -0.72 (0.11), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP E 473 HIS 0.003 0.001 HIS 2 809 PHE 0.017 0.001 PHE 2 520 TYR 0.018 0.001 TYR 5 730 ARG 0.010 0.000 ARG 2 749 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 284 time to evaluate : 6.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 726 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: 7 433 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8176 (mt) REVERT: 7 600 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8132 (ptp) REVERT: A 14 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8823 (ttmm) REVERT: B 63 MET cc_start: 0.9417 (mtm) cc_final: 0.8874 (mtp) REVERT: B 144 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8609 (mttm) REVERT: F 668 MET cc_start: 0.6317 (ptm) cc_final: 0.6016 (pmm) REVERT: F 778 MET cc_start: 0.4518 (mmt) cc_final: 0.4127 (mmm) REVERT: G 726 MET cc_start: 0.2976 (ttt) cc_final: 0.2744 (ttp) REVERT: G 778 MET cc_start: 0.2453 (mmt) cc_final: 0.0663 (mmt) REVERT: H 477 MET cc_start: 0.6241 (mpp) cc_final: 0.5578 (mpp) REVERT: H 659 MET cc_start: 0.6088 (tmm) cc_final: 0.5858 (tmm) REVERT: H 731 MET cc_start: 0.4922 (mpp) cc_final: 0.4538 (pmm) REVERT: K 675 TYR cc_start: 0.4353 (OUTLIER) cc_final: 0.4137 (t80) REVERT: M 1366 MET cc_start: 0.5130 (tpp) cc_final: 0.4440 (mmm) REVERT: M 1535 MET cc_start: 0.5238 (pmm) cc_final: 0.4752 (pmm) REVERT: M 2107 LEU cc_start: 0.9096 (tt) cc_final: 0.8882 (tp) outliers start: 84 outliers final: 73 residues processed: 358 average time/residue: 0.6588 time to fit residues: 421.0610 Evaluate side-chains 356 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 277 time to evaluate : 6.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 303 ILE Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 20 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 481 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 652 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 571 SER Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 4 residue 916 VAL Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 511 ASP Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 668 ILE Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 433 LEU Chi-restraints excluded: chain 7 residue 435 LEU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 542 GLU Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 502 LEU Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain G residue 723 ASP Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 566 SER Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1432 THR Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1838 ASN Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 546 optimal weight: 0.3980 chunk 733 optimal weight: 7.9990 chunk 210 optimal weight: 0.8980 chunk 634 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 689 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 708 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.132032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080824 restraints weight = 161110.722| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.84 r_work: 0.3085 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.190 72027 Z= 0.192 Angle : 0.539 59.169 97672 Z= 0.290 Chirality : 0.040 0.963 11156 Planarity : 0.003 0.059 12268 Dihedral : 10.000 150.479 10133 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.06 % Allowed : 13.81 % Favored : 85.13 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 8553 helix: 1.48 (0.09), residues: 3624 sheet: -1.03 (0.15), residues: 1284 loop : -0.71 (0.11), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP E 473 HIS 0.003 0.001 HIS 2 809 PHE 0.015 0.001 PHE 2 520 TYR 0.016 0.001 TYR 2 555 ARG 0.014 0.000 ARG 2 749 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12184.01 seconds wall clock time: 217 minutes 50.80 seconds (13070.80 seconds total)