Starting phenix.real_space_refine on Sun Mar 10 17:54:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/03_2024/6rwe_10038.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/03_2024/6rwe_10038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/03_2024/6rwe_10038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/03_2024/6rwe_10038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/03_2024/6rwe_10038.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/03_2024/6rwe_10038.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 94 5.49 5 S 241 5.16 5 C 33829 2.51 5 N 9268 2.21 5 O 10279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M ARG 316": "NH1" <-> "NH2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 6": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "O PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "Q TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 216": "OE1" <-> "OE2" Residue "Q ARG 305": "NH1" <-> "NH2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q ARG 350": "NH1" <-> "NH2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 411": "NH1" <-> "NH2" Residue "Q ARG 421": "NH1" <-> "NH2" Residue "Q ARG 478": "NH1" <-> "NH2" Residue "Q ARG 504": "NH1" <-> "NH2" Residue "S ARG 44": "NH1" <-> "NH2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S ARG 221": "NH1" <-> "NH2" Residue "S ARG 257": "NH1" <-> "NH2" Residue "S GLU 290": "OE1" <-> "OE2" Residue "S ARG 377": "NH1" <-> "NH2" Residue "S ARG 407": "NH1" <-> "NH2" Residue "S ARG 419": "NH1" <-> "NH2" Residue "S ARG 434": "NH1" <-> "NH2" Residue "S ARG 472": "NH1" <-> "NH2" Residue "S ARG 484": "NH1" <-> "NH2" Residue "S ARG 542": "NH1" <-> "NH2" Residue "S ARG 746": "NH1" <-> "NH2" Residue "S ARG 762": "NH1" <-> "NH2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 29": "NH1" <-> "NH2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 209": "NH1" <-> "NH2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 381": "NH1" <-> "NH2" Residue "R ARG 397": "NH1" <-> "NH2" Residue "R ARG 441": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53719 Number of models: 1 Model: "" Number of chains: 26 Chain: "T" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1000 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "U" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 944 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "M" Number of atoms: 3100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3100 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 11558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1464, 11558 Classifications: {'peptide': 1464} Link IDs: {'PTRANS': 59, 'TRANS': 1404} Chain breaks: 7 Chain: "B" Number of atoms: 9371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9371 Classifications: {'peptide': 1180} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 59, 'TRANS': 1120} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1576 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4086 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 485} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "Q" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3936 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4963 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 7 Chain: "R" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2771 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5480 SG CYS A 62 90.649 71.327 58.465 1.00 86.36 S ATOM 5499 SG CYS A 65 88.913 67.533 59.204 1.00 74.93 S ATOM 5800 SG CYS A 102 133.400 53.724 81.383 1.00106.46 S ATOM 5825 SG CYS A 105 132.423 50.643 79.363 1.00106.37 S ATOM 6624 SG CYS A 233 133.602 49.473 82.508 1.00111.28 S ATOM 6646 SG CYS A 236 136.439 50.656 80.543 1.00116.24 S ATOM 25261 SG CYS B1104 93.520 52.929 62.398 1.00 64.64 S ATOM 25287 SG CYS B1107 96.088 54.773 64.818 1.00 66.68 S ATOM 25434 SG CYS B1128 95.049 56.587 61.849 1.00 73.77 S ATOM 25462 SG CYS B1131 97.233 52.913 61.324 1.00 75.79 S ATOM 34235 SG CYS I 10 142.893 102.736 130.494 1.00 88.33 S ATOM 34257 SG CYS I 13 141.127 103.758 127.411 1.00 89.40 S ATOM 34377 SG CYS I 30 142.830 101.228 125.524 1.00104.19 S ATOM 34805 SG CYS I 86 73.986 53.941 131.960 1.00202.27 S ATOM 34827 SG CYS I 89 74.211 51.292 135.189 1.00209.68 S ATOM 35025 SG CYS I 114 76.165 55.361 134.566 1.00185.20 S ATOM 35044 SG CYS I 117 77.515 52.315 132.858 1.00196.97 S ATOM 35168 SG CYS J 7 46.492 96.096 111.429 1.00 39.96 S ATOM 35191 SG CYS J 10 42.784 95.566 111.950 1.00 40.75 S ATOM 35471 SG CYS J 45 44.902 94.593 114.738 1.00 39.91 S ATOM 36543 SG CYS L 31 71.469 120.827 84.243 1.00 54.18 S ATOM 36563 SG CYS L 34 69.604 124.444 84.886 1.00 56.73 S ATOM 36667 SG CYS L 48 71.105 123.746 81.554 1.00 59.29 S ATOM 36690 SG CYS L 51 73.593 124.020 84.426 1.00 59.19 S ATOM 42103 SG CYS Q 10 66.776 73.870 58.373 1.00112.27 S ATOM 42256 SG CYS Q 29 63.593 75.667 60.381 1.00 98.85 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P DT T 40 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 40 " occ=0.00 residue: pdb="ZN ZN I 202 " occ=0.75 Time building chain proxies: 19.88, per 1000 atoms: 0.37 Number of scatterers: 53719 At special positions: 0 Unit cell: (163.68, 213.84, 174.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 241 16.00 P 94 15.00 O 10279 8.00 N 9268 7.00 C 33829 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: 15.14 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 117 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb=" ZN Q 601 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 10 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 29 " Number of angles added : 24 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12252 Finding SS restraints... Secondary structure from input PDB file: 241 helices and 63 sheets defined 38.4% alpha, 14.6% beta 8 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 12.24 Creating SS restraints... Processing helix chain 'M' and resid 126 through 131 removed outlier: 4.086A pdb=" N ALA M 131 " --> pdb=" O ALA M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 145 Processing helix chain 'M' and resid 154 through 157 removed outlier: 3.597A pdb=" N SER M 157 " --> pdb=" O LEU M 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 154 through 157' Processing helix chain 'M' and resid 158 through 169 removed outlier: 4.241A pdb=" N VAL M 162 " --> pdb=" O ALA M 158 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER M 164 " --> pdb=" O ASP M 160 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL M 165 " --> pdb=" O ILE M 161 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N THR M 167 " --> pdb=" O ASP M 163 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.691A pdb=" N GLU M 180 " --> pdb=" O ALA M 176 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR M 182 " --> pdb=" O LEU M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 202 removed outlier: 3.593A pdb=" N TYR M 202 " --> pdb=" O VAL M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 208 removed outlier: 4.377A pdb=" N ILE M 207 " --> pdb=" O PRO M 203 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE M 208 " --> pdb=" O ILE M 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 203 through 208' Processing helix chain 'M' and resid 211 through 216 removed outlier: 3.665A pdb=" N GLN M 214 " --> pdb=" O LYS M 211 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE M 215 " --> pdb=" O GLU M 212 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE M 216 " --> pdb=" O LEU M 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 216' Processing helix chain 'M' and resid 218 through 223 removed outlier: 4.031A pdb=" N LEU M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS M 223 " --> pdb=" O SER M 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 218 through 223' Processing helix chain 'M' and resid 230 through 234 removed outlier: 3.784A pdb=" N LEU M 233 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE M 234 " --> pdb=" O LEU M 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 230 through 234' Processing helix chain 'M' and resid 252 through 257 removed outlier: 4.254A pdb=" N THR M 257 " --> pdb=" O SER M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 273 removed outlier: 3.555A pdb=" N LEU M 262 " --> pdb=" O LYS M 258 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU M 267 " --> pdb=" O TYR M 263 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY M 270 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL M 271 " --> pdb=" O LEU M 267 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR M 272 " --> pdb=" O LEU M 268 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 297 removed outlier: 4.105A pdb=" N ASP M 296 " --> pdb=" O GLU M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 323 No H-bonds generated for 'chain 'M' and resid 321 through 323' Processing helix chain 'M' and resid 324 through 340 removed outlier: 3.704A pdb=" N ILE M 328 " --> pdb=" O ASN M 324 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU M 329 " --> pdb=" O GLU M 325 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR M 331 " --> pdb=" O LYS M 327 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE M 335 " --> pdb=" O TYR M 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP M 340 " --> pdb=" O ILE M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 353 Processing helix chain 'M' and resid 356 through 365 removed outlier: 3.553A pdb=" N SER M 362 " --> pdb=" O SER M 358 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU M 363 " --> pdb=" O LYS M 359 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE M 364 " --> pdb=" O VAL M 360 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG M 365 " --> pdb=" O VAL M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 383 removed outlier: 3.757A pdb=" N PHE M 382 " --> pdb=" O ALA M 379 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY M 383 " --> pdb=" O GLU M 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 379 through 383' Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.738A pdb=" N ILE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 20 through 25' Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.515A pdb=" N GLY A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 43 " --> pdb=" O ASN A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 43' Processing helix chain 'A' and resid 91 through 99 removed outlier: 4.796A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.591A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.512A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.588A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 removed outlier: 3.524A pdb=" N LEU A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 removed outlier: 3.636A pdb=" N ILE A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.822A pdb=" N LYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.873A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.025A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.565A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.620A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.774A pdb=" N VAL A 503 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.822A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.695A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 652 through 656 removed outlier: 3.537A pdb=" N SER A 655 " --> pdb=" O ASN A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 681 removed outlier: 3.606A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.861A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.863A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.569A pdb=" N TYR A 759 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.501A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 824 removed outlier: 3.545A pdb=" N LEU A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.743A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.578A pdb=" N TRP A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 removed outlier: 4.096A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.868A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.616A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.652A pdb=" N VAL A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1011 removed outlier: 3.523A pdb=" N HIS A 998 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1027 removed outlier: 3.746A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.104A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A1107 " --> pdb=" O LYS A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 removed outlier: 3.508A pdb=" N GLN A1116 " --> pdb=" O HIS A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1163 through 1177 Processing helix chain 'A' and resid 1184 through 1192 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.894A pdb=" N ARG A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1257 removed outlier: 3.611A pdb=" N LYS A1256 " --> pdb=" O ASP A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.768A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1318 removed outlier: 3.528A pdb=" N LEU A1313 " --> pdb=" O SER A1309 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1335 removed outlier: 3.901A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1484 through 1494 removed outlier: 3.738A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.898A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.633A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1545 through 1553 removed outlier: 3.598A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.592A pdb=" N ASN A1567 " --> pdb=" O VAL A1563 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.627A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.724A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 Processing helix chain 'A' and resid 1636 through 1644 removed outlier: 3.574A pdb=" N ILE A1641 " --> pdb=" O PRO A1637 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 removed outlier: 3.532A pdb=" N ILE B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.033A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.808A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 63 removed outlier: 4.027A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.602A pdb=" N ILE B 68 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.763A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.536A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.665A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.568A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 317 Processing helix chain 'B' and resid 322 through 334 removed outlier: 4.400A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.666A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.576A pdb=" N LEU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.594A pdb=" N ALA B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 434 removed outlier: 3.640A pdb=" N LEU B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.667A pdb=" N ARG B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.565A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.807A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 573 through 577 removed outlier: 4.252A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.665A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.516A pdb=" N MET B 672 " --> pdb=" O GLN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.808A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.557A pdb=" N LEU B 703 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.673A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.805A pdb=" N HIS B 735 " --> pdb=" O ALA B 732 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 736 " --> pdb=" O LEU B 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 732 through 736' Processing helix chain 'B' and resid 754 through 758 removed outlier: 3.567A pdb=" N ASP B 758 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 812 through 815 removed outlier: 3.951A pdb=" N ARG B 815 " --> pdb=" O ALA B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 812 through 815' Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 960 through 976 Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.658A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.512A pdb=" N ARG B1076 " --> pdb=" O GLY B1072 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B1082 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1180 through 1191 removed outlier: 3.563A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.833A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.380A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.659A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.907A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.701A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 311 through 330 removed outlier: 3.566A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 4.149A pdb=" N THR D 8 " --> pdb=" O GLY D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.571A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.941A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 removed outlier: 3.767A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.600A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.983A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.704A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 142' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.924A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.748A pdb=" N HIS F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 102 removed outlier: 3.827A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 13 through 21 removed outlier: 4.639A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.655A pdb=" N VAL G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.788A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 133 removed outlier: 4.297A pdb=" N ASN H 131 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 removed outlier: 3.533A pdb=" N LYS I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.569A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 removed outlier: 3.623A pdb=" N ARG J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 51 through 54 removed outlier: 3.536A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.649A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 138 removed outlier: 3.504A pdb=" N LEU K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 removed outlier: 3.710A pdb=" N ARG N 154 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 54 Processing helix chain 'O' and resid 55 through 61 Processing helix chain 'O' and resid 70 through 78 removed outlier: 3.787A pdb=" N ILE O 74 " --> pdb=" O GLN O 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN O 77 " --> pdb=" O ILE O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 103 removed outlier: 4.002A pdb=" N ASN O 94 " --> pdb=" O ASP O 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE O 95 " --> pdb=" O LYS O 91 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE O 99 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.538A pdb=" N GLN O 117 " --> pdb=" O THR O 113 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER O 118 " --> pdb=" O PHE O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 128 removed outlier: 3.852A pdb=" N LEU O 128 " --> pdb=" O TRP O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 147 removed outlier: 4.518A pdb=" N LYS O 135 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR O 138 " --> pdb=" O SER O 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER O 145 " --> pdb=" O LYS O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 161 removed outlier: 3.983A pdb=" N MET O 156 " --> pdb=" O GLN O 152 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 183 removed outlier: 3.761A pdb=" N HIS O 173 " --> pdb=" O THR O 169 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP O 174 " --> pdb=" O VAL O 170 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR O 178 " --> pdb=" O ASP O 174 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG O 181 " --> pdb=" O LYS O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 197 removed outlier: 3.568A pdb=" N ILE O 190 " --> pdb=" O SER O 186 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP O 191 " --> pdb=" O MET O 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR O 192 " --> pdb=" O GLY O 188 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR O 193 " --> pdb=" O PHE O 189 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA O 195 " --> pdb=" O ASP O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 221 removed outlier: 3.575A pdb=" N ASN O 210 " --> pdb=" O ARG O 206 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY O 220 " --> pdb=" O LEU O 216 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 242 removed outlier: 3.840A pdb=" N LEU O 232 " --> pdb=" O GLN O 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS O 236 " --> pdb=" O LEU O 232 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 346 removed outlier: 4.715A pdb=" N LYS O 331 " --> pdb=" O GLU O 327 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU O 336 " --> pdb=" O LEU O 332 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU O 338 " --> pdb=" O SER O 334 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 369 removed outlier: 3.780A pdb=" N PHE O 361 " --> pdb=" O GLY O 357 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU O 364 " --> pdb=" O VAL O 360 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU O 367 " --> pdb=" O THR O 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 381 through 389 removed outlier: 4.304A pdb=" N MET O 385 " --> pdb=" O ILE O 381 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 397 removed outlier: 3.793A pdb=" N MET O 396 " --> pdb=" O GLN O 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 399 through 409 removed outlier: 3.694A pdb=" N ALA O 409 " --> pdb=" O ASP O 405 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 429 removed outlier: 3.795A pdb=" N LYS O 419 " --> pdb=" O GLU O 415 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER O 420 " --> pdb=" O LYS O 416 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU O 421 " --> pdb=" O LYS O 417 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER O 426 " --> pdb=" O GLN O 422 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA O 429 " --> pdb=" O GLY O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 453 removed outlier: 3.708A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU O 450 " --> pdb=" O LEU O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 458 through 462 removed outlier: 4.030A pdb=" N VAL O 461 " --> pdb=" O GLU O 458 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP O 462 " --> pdb=" O GLU O 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 458 through 462' Processing helix chain 'O' and resid 470 through 485 removed outlier: 3.597A pdb=" N ALA O 476 " --> pdb=" O HIS O 472 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE O 483 " --> pdb=" O ALA O 479 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE O 484 " --> pdb=" O LEU O 480 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS O 485 " --> pdb=" O CYS O 481 " (cutoff:3.500A) Processing helix chain 'O' and resid 504 through 511 Processing helix chain 'O' and resid 515 through 520 removed outlier: 3.903A pdb=" N PHE O 519 " --> pdb=" O ASN O 515 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N CYS O 520 " --> pdb=" O PRO O 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 515 through 520' Processing helix chain 'O' and resid 521 through 534 removed outlier: 3.556A pdb=" N MET O 527 " --> pdb=" O ASN O 523 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE O 528 " --> pdb=" O VAL O 524 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA O 529 " --> pdb=" O MET O 525 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG O 530 " --> pdb=" O LEU O 526 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 546 removed outlier: 3.525A pdb=" N GLU O 545 " --> pdb=" O PHE O 541 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 587 Processing helix chain 'O' and resid 599 through 607 removed outlier: 3.874A pdb=" N ILE O 604 " --> pdb=" O LYS O 600 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU O 605 " --> pdb=" O ASN O 601 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 82 Processing helix chain 'Q' and resid 85 through 90 removed outlier: 3.818A pdb=" N LYS Q 90 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 123 removed outlier: 3.665A pdb=" N LEU Q 102 " --> pdb=" O HIS Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 147 removed outlier: 4.228A pdb=" N HIS Q 131 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE Q 135 " --> pdb=" O HIS Q 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE Q 136 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN Q 147 " --> pdb=" O THR Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 171 removed outlier: 3.691A pdb=" N LEU Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 187 removed outlier: 3.607A pdb=" N THR Q 187 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 3.994A pdb=" N ILE Q 198 " --> pdb=" O GLN Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 207 removed outlier: 4.416A pdb=" N GLN Q 206 " --> pdb=" O SER Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 215 Processing helix chain 'Q' and resid 224 through 237 Processing helix chain 'Q' and resid 248 through 260 removed outlier: 3.514A pdb=" N LEU Q 253 " --> pdb=" O CYS Q 249 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Q 254 " --> pdb=" O GLN Q 250 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS Q 255 " --> pdb=" O GLY Q 251 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 277 removed outlier: 4.083A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS Q 271 " --> pdb=" O TYR Q 267 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN Q 272 " --> pdb=" O PHE Q 268 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 320 removed outlier: 3.574A pdb=" N VAL Q 306 " --> pdb=" O ALA Q 302 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU Q 307 " --> pdb=" O GLU Q 303 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER Q 308 " --> pdb=" O LEU Q 304 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU Q 318 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 332 removed outlier: 3.701A pdb=" N ILE Q 331 " --> pdb=" O PRO Q 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 334 through 339 Processing helix chain 'Q' and resid 344 through 357 removed outlier: 3.535A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR Q 357 " --> pdb=" O VAL Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 369 removed outlier: 3.946A pdb=" N PHE Q 367 " --> pdb=" O SER Q 364 " (cutoff:3.500A) Processing helix chain 'Q' and resid 370 through 381 removed outlier: 3.559A pdb=" N THR Q 374 " --> pdb=" O SER Q 370 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE Q 377 " --> pdb=" O GLU Q 373 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 384 No H-bonds generated for 'chain 'Q' and resid 382 through 384' Processing helix chain 'Q' and resid 406 through 417 removed outlier: 4.314A pdb=" N ARG Q 410 " --> pdb=" O GLN Q 406 " (cutoff:3.500A) Processing helix chain 'Q' and resid 437 through 446 removed outlier: 4.270A pdb=" N LEU Q 442 " --> pdb=" O PHE Q 438 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN Q 443 " --> pdb=" O ILE Q 439 " (cutoff:3.500A) Processing helix chain 'Q' and resid 471 through 492 removed outlier: 3.838A pdb=" N ALA Q 475 " --> pdb=" O ALA Q 471 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY Q 477 " --> pdb=" O LYS Q 473 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG Q 478 " --> pdb=" O GLU Q 474 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR Q 481 " --> pdb=" O GLY Q 477 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS Q 482 " --> pdb=" O ARG Q 478 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL Q 489 " --> pdb=" O SER Q 485 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP Q 490 " --> pdb=" O GLN Q 486 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE Q 491 " --> pdb=" O LEU Q 487 " (cutoff:3.500A) Processing helix chain 'Q' and resid 495 through 510 removed outlier: 3.675A pdb=" N ASP Q 500 " --> pdb=" O GLU Q 496 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS Q 501 " --> pdb=" O GLN Q 497 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE Q 505 " --> pdb=" O CYS Q 501 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA Q 508 " --> pdb=" O ARG Q 504 " (cutoff:3.500A) Processing helix chain 'Q' and resid 511 through 513 No H-bonds generated for 'chain 'Q' and resid 511 through 513' Processing helix chain 'S' and resid 189 through 195 Processing helix chain 'S' and resid 571 through 576 Processing helix chain 'S' and resid 589 through 607 removed outlier: 4.499A pdb=" N ARG S 601 " --> pdb=" O LYS S 597 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER S 605 " --> pdb=" O ARG S 601 " (cutoff:3.500A) Processing helix chain 'S' and resid 607 through 612 removed outlier: 3.604A pdb=" N GLU S 612 " --> pdb=" O GLN S 608 " (cutoff:3.500A) Processing helix chain 'S' and resid 616 through 644 removed outlier: 4.369A pdb=" N SER S 631 " --> pdb=" O GLY S 627 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE S 632 " --> pdb=" O TYR S 628 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA S 633 " --> pdb=" O ARG S 629 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU S 639 " --> pdb=" O ASN S 635 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER S 640 " --> pdb=" O GLU S 636 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN S 642 " --> pdb=" O LEU S 638 " (cutoff:3.500A) Processing helix chain 'S' and resid 671 through 685 removed outlier: 3.581A pdb=" N SER S 677 " --> pdb=" O PRO S 673 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU S 678 " --> pdb=" O GLU S 674 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU S 679 " --> pdb=" O PHE S 675 " (cutoff:3.500A) Processing helix chain 'S' and resid 699 through 703 removed outlier: 3.847A pdb=" N LEU S 702 " --> pdb=" O LEU S 699 " (cutoff:3.500A) Processing helix chain 'S' and resid 713 through 720 Processing helix chain 'S' and resid 732 through 742 removed outlier: 3.820A pdb=" N LYS S 738 " --> pdb=" O LYS S 734 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 765 removed outlier: 3.931A pdb=" N ILE S 756 " --> pdb=" O LEU S 752 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN S 757 " --> pdb=" O PHE S 753 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN S 758 " --> pdb=" O GLU S 754 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 38 removed outlier: 3.604A pdb=" N TYR R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG R 33 " --> pdb=" O ARG R 29 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 158 through 166 removed outlier: 4.095A pdb=" N LYS R 164 " --> pdb=" O HIS R 160 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU R 166 " --> pdb=" O PHE R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 174 Processing helix chain 'R' and resid 181 through 192 Processing helix chain 'R' and resid 209 through 226 removed outlier: 3.643A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 240 removed outlier: 3.973A pdb=" N LYS R 234 " --> pdb=" O SER R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 253 removed outlier: 3.710A pdb=" N LEU R 250 " --> pdb=" O GLN R 246 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 246 through 253' Processing helix chain 'R' and resid 267 through 278 removed outlier: 3.501A pdb=" N LEU R 271 " --> pdb=" O GLY R 267 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE R 277 " --> pdb=" O TRP R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 299 removed outlier: 4.040A pdb=" N GLN R 298 " --> pdb=" O VAL R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 323 removed outlier: 3.760A pdb=" N CYS R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 355 Processing helix chain 'R' and resid 362 through 380 removed outlier: 3.947A pdb=" N HIS R 372 " --> pdb=" O TYR R 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 421 removed outlier: 4.367A pdb=" N ASN R 402 " --> pdb=" O ASP R 398 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL R 404 " --> pdb=" O LYS R 400 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS R 406 " --> pdb=" O ASN R 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS R 407 " --> pdb=" O GLN R 403 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 441 removed outlier: 3.945A pdb=" N SER R 437 " --> pdb=" O ASN R 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 70 through 71 removed outlier: 7.270A pdb=" N LEU M 90 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL M 15 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS N 135 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE N 137 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 139 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLU N 141 " --> pdb=" O PRO N 59 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP N 92 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 101 through 102 removed outlier: 5.696A pdb=" N PHE M 51 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU M 56 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 101 through 102 removed outlier: 6.935A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 304 through 305 removed outlier: 4.877A pdb=" N VAL M 304 " --> pdb=" O PHE M 319 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE M 319 " --> pdb=" O VAL M 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'M' and resid 344 through 345 removed outlier: 3.557A pdb=" N LYS M 372 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR M 396 " --> pdb=" O ILE M 370 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE M 370 " --> pdb=" O THR M 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.699A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 80 through 86 removed outlier: 9.989A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A 85 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 476 removed outlier: 3.892A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 3.598A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.256A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB5, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.533A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.625A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.625A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB9, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.686A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 3.763A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.716A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1460 through 1462 removed outlier: 3.827A pdb=" N CYS A1470 " --> pdb=" O MET A1294 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.866A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.461A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 29 through 30 removed outlier: 7.120A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.028A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.960A pdb=" N ARG B 119 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AC9, first strand: chain 'B' and resid 400 through 403 Processing sheet with id=AD1, first strand: chain 'B' and resid 229 through 239 removed outlier: 5.338A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD3, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD4, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.793A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.523A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.523A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD8, first strand: chain 'B' and resid 857 through 863 removed outlier: 3.873A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1052 through 1053 removed outlier: 6.652A pdb=" N VAL B1052 " --> pdb=" O ASN Q 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AE2, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AE3, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AE4, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.684A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.684A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.366A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE8, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.750A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AF1, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.360A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.547A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.604A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 132 through 135 removed outlier: 5.297A pdb=" N ASP G 246 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL G 236 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER G 244 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE G 139 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU G 148 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE G 137 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.714A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF7, first strand: chain 'I' and resid 94 through 99 removed outlier: 3.628A pdb=" N THR I 109 " --> pdb=" O LEU I 99 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 49 through 50 removed outlier: 4.568A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 5 through 6 Processing sheet with id=AG1, first strand: chain 'S' and resid 63 through 66 removed outlier: 7.134A pdb=" N VAL S 547 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR S 548 " --> pdb=" O VAL S 539 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL S 539 " --> pdb=" O TYR S 548 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARG S 542 " --> pdb=" O PRO S 505 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 173 through 174 removed outlier: 3.521A pdb=" N TRP S 174 " --> pdb=" O GLU R 196 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 182 through 183 Processing sheet with id=AG4, first strand: chain 'S' and resid 186 through 187 Processing sheet with id=AG5, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.644A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN S 270 " --> pdb=" O ILE S 263 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG S 273 " --> pdb=" O SER S 287 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 300 through 303 removed outlier: 6.730A pdb=" N ASP S 319 " --> pdb=" O GLN S 301 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE S 326 " --> pdb=" O LEU S 347 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU S 347 " --> pdb=" O ILE S 326 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 362 through 365 removed outlier: 3.732A pdb=" N ARG S 362 " --> pdb=" O PHE S 375 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET S 380 " --> pdb=" O VAL S 393 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TRP S 389 " --> pdb=" O ASP S 384 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 402 through 404 removed outlier: 3.911A pdb=" N ILE S 421 " --> pdb=" O SER S 418 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 449 through 457 removed outlier: 3.566A pdb=" N HIS S 479 " --> pdb=" O ALA S 466 " (cutoff:3.500A) 1732 hydrogen bonds defined for protein. 4824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 19.79 Time building geometry restraints manager: 16.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9173 1.32 - 1.44: 14485 1.44 - 1.57: 30758 1.57 - 1.69: 185 1.69 - 1.81: 379 Bond restraints: 54980 Sorted by residual: bond pdb=" O3' DA T 49 " pdb=" P DC T 50 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.29e+01 bond pdb=" C GLU Q 292 " pdb=" N ARG Q 293 " ideal model delta sigma weight residual 1.331 1.391 -0.059 1.78e-02 3.16e+03 1.12e+01 bond pdb=" N ILE Q 281 " pdb=" CA ILE Q 281 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" C PRO S 291 " pdb=" O PRO S 291 " ideal model delta sigma weight residual 1.233 1.196 0.037 1.13e-02 7.83e+03 1.08e+01 bond pdb=" N HIS Q 98 " pdb=" CA HIS Q 98 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.44e+00 ... (remaining 54975 not shown) Histogram of bond angle deviations from ideal: 95.29 - 103.33: 761 103.33 - 111.38: 22959 111.38 - 119.43: 23565 119.43 - 127.47: 26774 127.47 - 135.52: 627 Bond angle restraints: 74686 Sorted by residual: angle pdb=" O3' DA T 49 " pdb=" P DC T 50 " pdb=" O5' DC T 50 " ideal model delta sigma weight residual 104.00 115.54 -11.54 1.50e+00 4.44e-01 5.92e+01 angle pdb=" N VAL J 14 " pdb=" CA VAL J 14 " pdb=" C VAL J 14 " ideal model delta sigma weight residual 113.53 107.64 5.89 9.80e-01 1.04e+00 3.61e+01 angle pdb=" N PRO R 295 " pdb=" CA PRO R 295 " pdb=" C PRO R 295 " ideal model delta sigma weight residual 110.70 117.74 -7.04 1.22e+00 6.72e-01 3.33e+01 angle pdb=" O GLU Q 292 " pdb=" C GLU Q 292 " pdb=" N ARG Q 293 " ideal model delta sigma weight residual 122.72 116.25 6.47 1.15e+00 7.56e-01 3.17e+01 angle pdb=" C GLU Q 292 " pdb=" N ARG Q 293 " pdb=" CA ARG Q 293 " ideal model delta sigma weight residual 122.31 132.22 -9.91 1.81e+00 3.05e-01 3.00e+01 ... (remaining 74681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 32612 35.75 - 71.51: 545 71.51 - 107.26: 38 107.26 - 143.01: 3 143.01 - 178.76: 9 Dihedral angle restraints: 33207 sinusoidal: 14319 harmonic: 18888 Sorted by residual: dihedral pdb=" CA ASP Q 431 " pdb=" C ASP Q 431 " pdb=" N SER Q 432 " pdb=" CA SER Q 432 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LEU A 669 " pdb=" C LEU A 669 " pdb=" N ILE A 670 " pdb=" CA ILE A 670 " ideal model delta harmonic sigma weight residual -180.00 -151.76 -28.24 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ILE B 199 " pdb=" C ILE B 199 " pdb=" N GLU B 200 " pdb=" CA GLU B 200 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 33204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 7711 0.104 - 0.209: 592 0.209 - 0.313: 36 0.313 - 0.418: 12 0.418 - 0.522: 1 Chirality restraints: 8352 Sorted by residual: chirality pdb=" CB ILE R 175 " pdb=" CA ILE R 175 " pdb=" CG1 ILE R 175 " pdb=" CG2 ILE R 175 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" CB ILE R 168 " pdb=" CA ILE R 168 " pdb=" CG1 ILE R 168 " pdb=" CG2 ILE R 168 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C3' DC T 12 " pdb=" C4' DC T 12 " pdb=" O3' DC T 12 " pdb=" C2' DC T 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.27 -0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 8349 not shown) Planarity restraints: 9248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 628 " 0.026 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE A 628 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 628 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 628 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 628 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 628 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 628 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 127 " 0.048 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO E 128 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 368 " -0.019 2.00e-02 2.50e+03 2.04e-02 8.31e+00 pdb=" CG TYR R 368 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR R 368 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR R 368 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR R 368 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 368 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR R 368 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 368 " 0.003 2.00e-02 2.50e+03 ... (remaining 9245 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 369 2.56 - 3.14: 40203 3.14 - 3.73: 80630 3.73 - 4.31: 116970 4.31 - 4.90: 190520 Nonbonded interactions: 428692 Sorted by model distance: nonbonded pdb=" OD1 ASN S 31 " pdb=" N TYR S 32 " model vdw 1.975 2.520 nonbonded pdb=" ND2 ASN Q 14 " pdb="ZN ZN Q 601 " model vdw 2.089 2.310 nonbonded pdb=" N GLU R 204 " pdb=" OE1 GLU R 204 " model vdw 2.161 2.520 nonbonded pdb=" O GLY R 194 " pdb=" O LEU R 195 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR O 423 " pdb=" OH TYR O 594 " model vdw 2.207 2.440 ... (remaining 428687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.860 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 118.100 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.120 54980 Z= 0.587 Angle : 1.024 11.545 74686 Z= 0.565 Chirality : 0.062 0.522 8352 Planarity : 0.007 0.074 9248 Dihedral : 13.234 178.764 20955 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.45 % Favored : 92.47 % Rotamer: Outliers : 0.73 % Allowed : 3.28 % Favored : 95.99 % Cbeta Deviations : 0.02 % 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: -4.84 (0.08), residues: 6352 helix: -4.18 (0.05), residues: 2214 sheet: -2.54 (0.17), residues: 756 loop : -2.67 (0.09), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP Q 20 HIS 0.024 0.003 HIS B 532 PHE 0.054 0.003 PHE A 628 TYR 0.049 0.003 TYR R 368 ARG 0.021 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1281 time to evaluate : 4.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 28 LYS cc_start: 0.2158 (mtpp) cc_final: 0.1814 (tttp) REVERT: M 100 VAL cc_start: 0.2328 (t) cc_final: 0.1880 (t) REVERT: M 111 PRO cc_start: 0.6186 (Cg_endo) cc_final: 0.5930 (Cg_exo) REVERT: M 337 MET cc_start: 0.1322 (ttm) cc_final: 0.1047 (pp-130) REVERT: M 397 MET cc_start: 0.2416 (mtt) cc_final: 0.1946 (mtm) REVERT: A 15 ASP cc_start: 0.5425 (m-30) cc_final: 0.4183 (m-30) REVERT: A 325 ASP cc_start: 0.4674 (t0) cc_final: 0.4266 (p0) REVERT: A 697 TYR cc_start: 0.3179 (t80) cc_final: 0.2663 (t80) REVERT: A 1541 ILE cc_start: 0.4150 (pt) cc_final: 0.3308 (pt) REVERT: A 1546 VAL cc_start: 0.4098 (t) cc_final: 0.2257 (m) REVERT: B 152 LEU cc_start: 0.2764 (mp) cc_final: 0.2507 (mt) REVERT: B 345 SER cc_start: 0.5151 (p) cc_final: 0.4859 (t) REVERT: C 301 ASN cc_start: 0.3751 (t0) cc_final: 0.3400 (m-40) REVERT: D 1 MET cc_start: 0.1306 (ptm) cc_final: 0.0575 (ttm) REVERT: E 98 ILE cc_start: 0.7687 (mt) cc_final: 0.7347 (mp) REVERT: G 16 PHE cc_start: 0.6018 (t80) cc_final: 0.5142 (m-80) REVERT: H 78 SER cc_start: 0.6062 (p) cc_final: 0.5717 (m) REVERT: H 102 TYR cc_start: 0.3725 (p90) cc_final: 0.2822 (p90) REVERT: K 81 MET cc_start: 0.2035 (mmm) cc_final: 0.0504 (ppp) REVERT: O 71 ILE cc_start: 0.3695 (mm) cc_final: 0.3210 (pt) REVERT: O 100 LEU cc_start: 0.5938 (mt) cc_final: 0.5340 (mt) REVERT: O 124 LYS cc_start: 0.6629 (mmtp) cc_final: 0.5293 (mtpt) REVERT: O 163 ILE cc_start: 0.5722 (OUTLIER) cc_final: 0.5340 (pt) REVERT: O 221 TYR cc_start: 0.3379 (m-80) cc_final: 0.3058 (m-80) REVERT: O 449 TRP cc_start: 0.5946 (t60) cc_final: 0.5363 (t60) REVERT: O 490 ILE cc_start: 0.3897 (mp) cc_final: 0.3679 (tp) REVERT: O 582 ARG cc_start: 0.4000 (tpt90) cc_final: 0.3548 (mtp-110) REVERT: Q 85 GLN cc_start: 0.1811 (pp30) cc_final: 0.1235 (tm-30) REVERT: Q 240 LYS cc_start: 0.6277 (mmmt) cc_final: 0.5334 (mppt) REVERT: Q 351 ASN cc_start: 0.4610 (m-40) cc_final: 0.4352 (m110) REVERT: Q 421 ARG cc_start: 0.4243 (ttt180) cc_final: 0.3885 (tpm170) REVERT: Q 490 ASP cc_start: 0.2912 (m-30) cc_final: 0.1938 (t0) REVERT: S 16 LEU cc_start: 0.5766 (tm) cc_final: 0.4919 (pp) REVERT: S 32 TYR cc_start: 0.4878 (m-10) cc_final: 0.4618 (t80) REVERT: S 39 LYS cc_start: 0.3759 (mmtp) cc_final: 0.3338 (pttt) REVERT: S 369 PHE cc_start: 0.5253 (t80) cc_final: 0.4877 (t80) REVERT: S 600 GLU cc_start: 0.6737 (tp30) cc_final: 0.5774 (tm-30) REVERT: S 671 SER cc_start: 0.5585 (t) cc_final: 0.5282 (m) REVERT: S 680 ASP cc_start: 0.6023 (m-30) cc_final: 0.5624 (p0) REVERT: S 692 THR cc_start: 0.2368 (p) cc_final: 0.1166 (p) REVERT: S 707 ASP cc_start: 0.3209 (t0) cc_final: 0.2631 (m-30) REVERT: S 736 ILE cc_start: 0.5363 (mt) cc_final: 0.5149 (pt) REVERT: S 749 LYS cc_start: 0.5486 (tttm) cc_final: 0.4997 (ptpt) REVERT: R 23 TYR cc_start: 0.6006 (t80) cc_final: 0.5641 (t80) REVERT: R 122 ASP cc_start: 0.6176 (t0) cc_final: 0.5932 (t70) REVERT: R 157 MET cc_start: 0.3184 (OUTLIER) cc_final: 0.2031 (tpt) REVERT: R 173 MET cc_start: 0.4512 (tpt) cc_final: 0.3580 (pp-130) outliers start: 42 outliers final: 12 residues processed: 1313 average time/residue: 1.1757 time to fit residues: 1992.6203 Evaluate side-chains 661 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 647 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 202 ASN Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain Q residue 206 GLN Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 377 ARG Chi-restraints excluded: chain R residue 157 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 546 optimal weight: 0.1980 chunk 490 optimal weight: 0.6980 chunk 272 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 330 optimal weight: 0.0870 chunk 261 optimal weight: 0.6980 chunk 507 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 377 optimal weight: 1.9990 chunk 587 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 54 HIS M 89 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A1047 GLN ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1527 GLN B 209 GLN B 235 GLN B 248 ASN B 423 ASN B 492 ASN B 504 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN B 673 ASN B 764 ASN ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 GLN B1165 ASN C 130 ASN D 88 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 64 GLN G 65 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 134 ASN I 97 HIS L 53 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** O 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 422 GLN O 438 GLN O 584 GLN Q 33 HIS ** Q 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 294 HIS S 388 ASN S 395 GLN S 720 GLN R 298 GLN R 402 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3887 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 54980 Z= 0.243 Angle : 0.740 12.527 74686 Z= 0.387 Chirality : 0.046 0.414 8352 Planarity : 0.006 0.072 9248 Dihedral : 14.008 178.139 8060 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.35 % Favored : 94.63 % Rotamer: Outliers : 4.01 % Allowed : 12.71 % Favored : 83.28 % 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: -3.47 (0.09), residues: 6352 helix: -2.51 (0.09), residues: 2277 sheet: -2.01 (0.18), residues: 726 loop : -2.18 (0.10), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP Q 118 HIS 0.012 0.001 HIS B 532 PHE 0.034 0.002 PHE A 239 TYR 0.031 0.002 TYR A1302 ARG 0.015 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 838 time to evaluate : 4.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 71 GLN cc_start: 0.3725 (pm20) cc_final: 0.3437 (pp30) REVERT: M 91 TYR cc_start: 0.4005 (m-80) cc_final: 0.3271 (m-80) REVERT: M 111 PRO cc_start: 0.6249 (Cg_endo) cc_final: 0.6038 (Cg_exo) REVERT: M 397 MET cc_start: 0.2484 (mtt) cc_final: 0.2175 (mtm) REVERT: A 325 ASP cc_start: 0.5061 (t0) cc_final: 0.4296 (p0) REVERT: A 510 PRO cc_start: 0.5631 (Cg_exo) cc_final: 0.5428 (Cg_endo) REVERT: A 555 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6338 (ttmp) REVERT: A 611 GLU cc_start: 0.3935 (mt-10) cc_final: 0.3197 (mt-10) REVERT: A 1105 ARG cc_start: 0.5345 (ptp90) cc_final: 0.5093 (ptt180) REVERT: A 1485 MET cc_start: 0.2956 (tpt) cc_final: 0.2398 (tpt) REVERT: A 1588 MET cc_start: 0.6345 (tpt) cc_final: 0.6046 (mmt) REVERT: B 373 MET cc_start: 0.6567 (tmm) cc_final: 0.5981 (tmt) REVERT: B 461 MET cc_start: 0.5744 (mmm) cc_final: 0.4904 (mtt) REVERT: B 649 MET cc_start: 0.2730 (OUTLIER) cc_final: 0.2259 (mmm) REVERT: B 1155 ASP cc_start: 0.5436 (OUTLIER) cc_final: 0.5041 (p0) REVERT: D 46 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5237 (tt0) REVERT: D 94 ARG cc_start: 0.4241 (OUTLIER) cc_final: 0.3978 (tpm-80) REVERT: F 82 THR cc_start: 0.6338 (t) cc_final: 0.6100 (t) REVERT: F 134 ILE cc_start: 0.7139 (mm) cc_final: 0.6776 (mp) REVERT: G 16 PHE cc_start: 0.6684 (t80) cc_final: 0.5248 (m-80) REVERT: G 136 TYR cc_start: 0.5517 (OUTLIER) cc_final: 0.5269 (m-80) REVERT: H 6 PHE cc_start: 0.6777 (t80) cc_final: 0.6416 (t80) REVERT: H 78 SER cc_start: 0.6847 (p) cc_final: 0.6503 (m) REVERT: H 102 TYR cc_start: 0.4429 (p90) cc_final: 0.3773 (p90) REVERT: K 81 MET cc_start: 0.2018 (mmm) cc_final: 0.0667 (ptt) REVERT: N 74 PHE cc_start: 0.2958 (t80) cc_final: 0.2346 (t80) REVERT: O 100 LEU cc_start: 0.5501 (mt) cc_final: 0.5257 (mt) REVERT: O 124 LYS cc_start: 0.6709 (mmtp) cc_final: 0.6255 (mmtm) REVERT: O 131 HIS cc_start: 0.5997 (m-70) cc_final: 0.5687 (p-80) REVERT: O 200 ASN cc_start: 0.4097 (t0) cc_final: 0.3779 (t0) REVERT: O 206 ARG cc_start: 0.6088 (mmm160) cc_final: 0.5315 (mmm160) REVERT: O 449 TRP cc_start: 0.5510 (t60) cc_final: 0.5264 (t60) REVERT: O 582 ARG cc_start: 0.3977 (tpt90) cc_final: 0.3662 (mtp180) REVERT: Q 31 TYR cc_start: 0.4165 (m-80) cc_final: 0.3929 (m-80) REVERT: Q 74 GLN cc_start: 0.3114 (mt0) cc_final: 0.2852 (tp-100) REVERT: Q 79 GLN cc_start: 0.5715 (tm130) cc_final: 0.5469 (tm-30) REVERT: Q 154 LEU cc_start: 0.2117 (OUTLIER) cc_final: 0.1897 (tp) REVERT: Q 158 MET cc_start: 0.2514 (OUTLIER) cc_final: -0.1029 (pmm) REVERT: Q 200 PRO cc_start: 0.2513 (Cg_exo) cc_final: 0.2175 (Cg_endo) REVERT: Q 212 VAL cc_start: 0.5191 (OUTLIER) cc_final: 0.4966 (t) REVERT: Q 240 LYS cc_start: 0.6405 (mmmt) cc_final: 0.5671 (mppt) REVERT: Q 417 PHE cc_start: 0.6185 (m-80) cc_final: 0.5020 (m-80) REVERT: Q 421 ARG cc_start: 0.4264 (ttt180) cc_final: 0.3812 (ttm170) REVERT: S 16 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.4913 (pp) REVERT: S 45 PRO cc_start: 0.1648 (Cg_endo) cc_final: 0.1159 (Cg_exo) REVERT: S 238 LEU cc_start: 0.3411 (pt) cc_final: 0.3134 (mm) REVERT: S 304 ASP cc_start: 0.6257 (t0) cc_final: 0.5447 (m-30) REVERT: S 388 ASN cc_start: 0.5121 (t0) cc_final: 0.4104 (p0) REVERT: S 478 MET cc_start: 0.4675 (OUTLIER) cc_final: 0.2955 (tpt) REVERT: S 671 SER cc_start: 0.5245 (t) cc_final: 0.4949 (m) REVERT: S 680 ASP cc_start: 0.6104 (m-30) cc_final: 0.5526 (t0) REVERT: S 692 THR cc_start: 0.2279 (p) cc_final: 0.1187 (p) REVERT: S 707 ASP cc_start: 0.2368 (t0) cc_final: 0.1976 (m-30) REVERT: S 736 ILE cc_start: 0.4539 (mt) cc_final: 0.4185 (pt) REVERT: S 749 LYS cc_start: 0.5192 (tttm) cc_final: 0.4902 (ptmt) REVERT: R 122 ASP cc_start: 0.6474 (t0) cc_final: 0.5112 (t0) REVERT: R 173 MET cc_start: 0.5733 (tpt) cc_final: 0.5235 (tpt) outliers start: 232 outliers final: 61 residues processed: 981 average time/residue: 1.0974 time to fit residues: 1422.7207 Evaluate side-chains 695 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 623 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1000 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 454 VAL Chi-restraints excluded: chain O residue 527 MET Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 368 HIS Chi-restraints excluded: chain S residue 379 LYS Chi-restraints excluded: chain S residue 478 MET Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain S residue 765 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 326 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 489 optimal weight: 10.0000 chunk 400 optimal weight: 0.0970 chunk 162 optimal weight: 0.9990 chunk 588 optimal weight: 10.0000 chunk 635 optimal weight: 5.9990 chunk 524 optimal weight: 0.5980 chunk 583 optimal weight: 0.8980 chunk 200 optimal weight: 0.0470 chunk 472 optimal weight: 7.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 89 GLN A 221 HIS ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 535 GLN A 571 HIS ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1047 GLN ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 492 ASN B 504 HIS B 575 HIS B 686 HIS B 702 ASN ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN C 58 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN J 53 HIS K 64 GLN K 74 ASN O 342 HIS O 488 HIS Q 30 GLN Q 85 GLN Q 325 GLN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4570 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 54980 Z= 0.228 Angle : 0.697 16.125 74686 Z= 0.360 Chirality : 0.045 0.275 8352 Planarity : 0.005 0.128 9248 Dihedral : 13.792 178.565 8038 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.81 % Favored : 94.18 % Rotamer: Outliers : 3.90 % Allowed : 15.63 % Favored : 80.46 % 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: -2.68 (0.10), residues: 6352 helix: -1.47 (0.10), residues: 2276 sheet: -1.67 (0.17), residues: 784 loop : -2.01 (0.10), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 760 HIS 0.017 0.001 HIS E 147 PHE 0.033 0.002 PHE A1570 TYR 0.027 0.002 TYR O 193 ARG 0.012 0.001 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 832 time to evaluate : 4.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 89 GLN cc_start: 0.3751 (OUTLIER) cc_final: 0.3255 (pp30) REVERT: A 59 ARG cc_start: 0.6889 (tpm170) cc_final: 0.5326 (mtp85) REVERT: A 63 SER cc_start: 0.3468 (p) cc_final: 0.2701 (m) REVERT: A 323 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6164 (tt) REVERT: A 325 ASP cc_start: 0.5461 (t0) cc_final: 0.4467 (p0) REVERT: A 572 THR cc_start: 0.6065 (m) cc_final: 0.5648 (p) REVERT: A 589 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6865 (mpt) REVERT: A 603 HIS cc_start: 0.6573 (m-70) cc_final: 0.6300 (m-70) REVERT: A 611 GLU cc_start: 0.4715 (mt-10) cc_final: 0.3620 (mt-10) REVERT: A 664 SER cc_start: 0.4749 (m) cc_final: 0.4344 (p) REVERT: A 687 PHE cc_start: 0.5505 (m-80) cc_final: 0.5254 (m-80) REVERT: A 928 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5707 (ttm) REVERT: A 1058 THR cc_start: 0.6247 (p) cc_final: 0.5804 (t) REVERT: A 1089 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5806 (pp) REVERT: A 1178 LEU cc_start: 0.4109 (OUTLIER) cc_final: 0.3810 (pt) REVERT: A 1485 MET cc_start: 0.3793 (tpt) cc_final: 0.3377 (tpp) REVERT: A 1620 GLN cc_start: 0.7188 (tp40) cc_final: 0.6829 (tm-30) REVERT: B 443 LYS cc_start: 0.6043 (tptp) cc_final: 0.5805 (tppt) REVERT: B 512 LEU cc_start: 0.6255 (mt) cc_final: 0.5821 (tp) REVERT: B 611 TRP cc_start: 0.5909 (m100) cc_final: 0.5207 (m100) REVERT: B 649 MET cc_start: 0.3184 (OUTLIER) cc_final: 0.2855 (mmm) REVERT: B 716 MET cc_start: 0.5064 (ppp) cc_final: 0.4301 (ptt) REVERT: B 1155 ASP cc_start: 0.5544 (OUTLIER) cc_final: 0.4981 (p0) REVERT: B 1158 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6488 (mt) REVERT: B 1198 TYR cc_start: 0.6573 (m-80) cc_final: 0.6182 (m-80) REVERT: C 71 MET cc_start: 0.5814 (mmt) cc_final: 0.5244 (mpt) REVERT: C 163 TYR cc_start: 0.5421 (m-80) cc_final: 0.5180 (m-80) REVERT: D 94 ARG cc_start: 0.4324 (OUTLIER) cc_final: 0.3960 (tpm-80) REVERT: E 52 ARG cc_start: 0.6002 (tmm-80) cc_final: 0.5636 (ttp80) REVERT: E 57 MET cc_start: 0.4748 (tmm) cc_final: 0.4447 (tmm) REVERT: E 93 MET cc_start: 0.6671 (tpp) cc_final: 0.6261 (tpp) REVERT: G 136 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.5400 (m-80) REVERT: H 102 TYR cc_start: 0.5171 (p90) cc_final: 0.4922 (p90) REVERT: H 130 ARG cc_start: 0.4667 (ptp90) cc_final: 0.4318 (ptp90) REVERT: K 62 SER cc_start: 0.6946 (OUTLIER) cc_final: 0.6633 (m) REVERT: L 42 ARG cc_start: 0.5367 (ptp-110) cc_final: 0.4748 (mtt-85) REVERT: N 90 MET cc_start: 0.4107 (OUTLIER) cc_final: 0.3357 (tmt) REVERT: O 71 ILE cc_start: 0.4028 (mm) cc_final: 0.3228 (pt) REVERT: O 100 LEU cc_start: 0.5600 (mt) cc_final: 0.5368 (mt) REVERT: O 124 LYS cc_start: 0.6044 (mmtp) cc_final: 0.4716 (mtpm) REVERT: O 157 ILE cc_start: 0.6622 (tt) cc_final: 0.6385 (tp) REVERT: O 206 ARG cc_start: 0.5975 (mmm160) cc_final: 0.5469 (mmm160) REVERT: O 385 MET cc_start: 0.7407 (tpp) cc_final: 0.7086 (tpp) REVERT: O 412 GLU cc_start: 0.5286 (mt-10) cc_final: 0.4909 (mp0) REVERT: O 526 LEU cc_start: 0.5383 (tp) cc_final: 0.4857 (pp) REVERT: O 582 ARG cc_start: 0.3806 (tpt90) cc_final: 0.3407 (mtp180) REVERT: Q 74 GLN cc_start: 0.3471 (mt0) cc_final: 0.2410 (tp40) REVERT: Q 79 GLN cc_start: 0.5601 (tm130) cc_final: 0.5256 (tm-30) REVERT: Q 139 LYS cc_start: 0.5363 (tttt) cc_final: 0.4476 (tptt) REVERT: Q 154 LEU cc_start: 0.3241 (OUTLIER) cc_final: 0.2677 (tp) REVERT: Q 155 GLN cc_start: 0.3235 (tp-100) cc_final: 0.2774 (mm-40) REVERT: Q 157 HIS cc_start: 0.3831 (t-90) cc_final: 0.3584 (t70) REVERT: Q 240 LYS cc_start: 0.6330 (mmmt) cc_final: 0.5606 (mttp) REVERT: Q 303 GLU cc_start: 0.4696 (mp0) cc_final: 0.4155 (mp0) REVERT: Q 421 ARG cc_start: 0.4326 (ttt180) cc_final: 0.3850 (ttm170) REVERT: Q 480 LEU cc_start: 0.5309 (OUTLIER) cc_final: 0.4935 (pp) REVERT: Q 513 MET cc_start: 0.0746 (mpt) cc_final: 0.0493 (pmm) REVERT: S 45 PRO cc_start: 0.1637 (Cg_endo) cc_final: 0.1038 (Cg_exo) REVERT: S 285 MET cc_start: 0.3649 (ppp) cc_final: 0.3276 (tpp) REVERT: S 304 ASP cc_start: 0.5911 (t0) cc_final: 0.5167 (m-30) REVERT: S 369 PHE cc_start: 0.4074 (t80) cc_final: 0.3841 (t80) REVERT: S 475 ARG cc_start: 0.1902 (OUTLIER) cc_final: 0.1326 (mtm110) REVERT: S 478 MET cc_start: 0.5143 (ptp) cc_final: 0.3552 (tpt) REVERT: S 678 LEU cc_start: 0.6570 (mt) cc_final: 0.6022 (tt) REVERT: S 692 THR cc_start: 0.2238 (p) cc_final: 0.1336 (p) REVERT: S 736 ILE cc_start: 0.4073 (mt) cc_final: 0.3550 (pp) REVERT: R 122 ASP cc_start: 0.6172 (t0) cc_final: 0.5777 (t0) REVERT: R 359 MET cc_start: 0.1935 (pmm) cc_final: 0.1576 (pmm) REVERT: R 409 HIS cc_start: 0.5502 (OUTLIER) cc_final: 0.4703 (p-80) outliers start: 226 outliers final: 73 residues processed: 983 average time/residue: 1.0690 time to fit residues: 1394.9028 Evaluate side-chains 712 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 622 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 337 MET Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 378 THR Chi-restraints excluded: chain O residue 488 HIS Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 481 THR Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 379 LYS Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 475 ARG Chi-restraints excluded: chain S residue 495 SER Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain S residue 714 PHE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 581 optimal weight: 6.9990 chunk 442 optimal weight: 0.0980 chunk 305 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 280 optimal weight: 0.8980 chunk 395 optimal weight: 10.0000 chunk 590 optimal weight: 10.0000 chunk 625 optimal weight: 7.9990 chunk 308 optimal weight: 0.7980 chunk 559 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 282 HIS B 492 ASN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 GLN B 896 GLN B1038 HIS B1199 ASN D 30 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 121 ASN O 131 HIS Q 85 GLN S 232 ASN S 348 HIS S 705 HIS R 221 HIS ** R 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5266 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 54980 Z= 0.247 Angle : 0.706 14.582 74686 Z= 0.361 Chirality : 0.045 0.274 8352 Planarity : 0.005 0.070 9248 Dihedral : 13.840 179.934 8035 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.28 % Allowed : 17.69 % Favored : 78.03 % Cbeta Deviations : 0.02 % 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: -2.27 (0.10), residues: 6352 helix: -1.03 (0.10), residues: 2290 sheet: -1.48 (0.18), residues: 727 loop : -1.85 (0.10), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1469 HIS 0.050 0.001 HIS O 488 PHE 0.028 0.002 PHE O 486 TYR 0.028 0.002 TYR S 405 ARG 0.019 0.001 ARG O 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 867 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 89 GLN cc_start: 0.3137 (OUTLIER) cc_final: 0.2754 (pp30) REVERT: M 159 ILE cc_start: 0.4324 (OUTLIER) cc_final: 0.4085 (pp) REVERT: M 359 LYS cc_start: 0.4706 (tptp) cc_final: 0.3936 (tptt) REVERT: A 63 SER cc_start: 0.3995 (p) cc_final: 0.3493 (m) REVERT: A 329 ARG cc_start: 0.5693 (mmm160) cc_final: 0.5230 (tpp-160) REVERT: A 331 GLU cc_start: 0.3889 (OUTLIER) cc_final: 0.3613 (mp0) REVERT: A 611 GLU cc_start: 0.5874 (mt-10) cc_final: 0.4901 (mt-10) REVERT: A 977 MET cc_start: 0.4563 (OUTLIER) cc_final: 0.3885 (tpt) REVERT: A 1089 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.5901 (pp) REVERT: A 1178 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5047 (pt) REVERT: A 1248 ASP cc_start: 0.4115 (m-30) cc_final: 0.3797 (m-30) REVERT: A 1589 MET cc_start: 0.7017 (mmm) cc_final: 0.6654 (mpp) REVERT: A 1620 GLN cc_start: 0.7390 (tp40) cc_final: 0.7015 (tm-30) REVERT: B 443 LYS cc_start: 0.6379 (tptp) cc_final: 0.6060 (tppt) REVERT: B 512 LEU cc_start: 0.6239 (mt) cc_final: 0.5780 (tp) REVERT: B 672 MET cc_start: 0.2129 (OUTLIER) cc_final: 0.1151 (ptp) REVERT: B 716 MET cc_start: 0.5849 (ppp) cc_final: 0.5627 (ptp) REVERT: B 915 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6861 (m-30) REVERT: B 1022 LEU cc_start: 0.5656 (OUTLIER) cc_final: 0.5427 (mt) REVERT: B 1066 HIS cc_start: 0.5269 (t-90) cc_final: 0.4778 (m170) REVERT: B 1155 ASP cc_start: 0.5638 (OUTLIER) cc_final: 0.5256 (p0) REVERT: B 1198 TYR cc_start: 0.6990 (m-80) cc_final: 0.6703 (m-80) REVERT: C 71 MET cc_start: 0.6167 (mmt) cc_final: 0.5425 (mmm) REVERT: D 15 THR cc_start: 0.8203 (t) cc_final: 0.7910 (t) REVERT: E 93 MET cc_start: 0.6688 (tpp) cc_final: 0.6257 (tpp) REVERT: E 94 LYS cc_start: 0.6883 (mmmm) cc_final: 0.6489 (tmtt) REVERT: E 121 MET cc_start: 0.5363 (tpp) cc_final: 0.5146 (tpp) REVERT: E 123 LEU cc_start: 0.6191 (tp) cc_final: 0.5859 (tp) REVERT: F 116 ASP cc_start: 0.7391 (t0) cc_final: 0.7154 (t70) REVERT: F 122 MET cc_start: 0.6429 (ptp) cc_final: 0.5768 (ptm) REVERT: G 136 TYR cc_start: 0.5632 (OUTLIER) cc_final: 0.5307 (m-80) REVERT: G 234 ARG cc_start: 0.6852 (mtt-85) cc_final: 0.6522 (mmm160) REVERT: H 130 ARG cc_start: 0.4922 (ptp90) cc_final: 0.4549 (ptp90) REVERT: I 94 MET cc_start: 0.1317 (ttt) cc_final: 0.0521 (tmt) REVERT: L 42 ARG cc_start: 0.5747 (ptp-110) cc_final: 0.5084 (mtt-85) REVERT: L 64 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5822 (tt) REVERT: N 90 MET cc_start: 0.4436 (ttp) cc_final: 0.3369 (tmt) REVERT: O 99 ILE cc_start: 0.5510 (OUTLIER) cc_final: 0.5309 (pt) REVERT: O 124 LYS cc_start: 0.6471 (mmtp) cc_final: 0.5250 (mtpm) REVERT: O 157 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6639 (tp) REVERT: O 206 ARG cc_start: 0.6202 (mmm160) cc_final: 0.4820 (mpp-170) REVERT: O 337 THR cc_start: 0.4928 (m) cc_final: 0.4666 (p) REVERT: O 380 SER cc_start: 0.6207 (m) cc_final: 0.5811 (t) REVERT: O 582 ARG cc_start: 0.4014 (tpt90) cc_final: 0.3567 (mtp180) REVERT: O 584 GLN cc_start: 0.5841 (tp40) cc_final: 0.3830 (mp10) REVERT: Q 74 GLN cc_start: 0.2994 (mt0) cc_final: 0.2293 (tp40) REVERT: Q 79 GLN cc_start: 0.5778 (tm130) cc_final: 0.5382 (tm-30) REVERT: Q 139 LYS cc_start: 0.5773 (tttt) cc_final: 0.4807 (tptt) REVERT: Q 154 LEU cc_start: 0.2117 (OUTLIER) cc_final: 0.1718 (tt) REVERT: Q 240 LYS cc_start: 0.6483 (mmmt) cc_final: 0.5457 (mttp) REVERT: Q 241 GLU cc_start: 0.4349 (OUTLIER) cc_final: 0.3793 (pm20) REVERT: Q 258 MET cc_start: 0.5669 (ptt) cc_final: 0.5274 (ptm) REVERT: Q 303 GLU cc_start: 0.4479 (mp0) cc_final: 0.4130 (mp0) REVERT: Q 421 ARG cc_start: 0.4657 (ttt180) cc_final: 0.4000 (tpm170) REVERT: S 16 LEU cc_start: 0.5016 (tt) cc_final: 0.4662 (tt) REVERT: S 45 PRO cc_start: 0.1575 (Cg_endo) cc_final: 0.1036 (Cg_exo) REVERT: S 285 MET cc_start: 0.4136 (ppp) cc_final: 0.3862 (tpp) REVERT: S 451 ILE cc_start: 0.6007 (OUTLIER) cc_final: 0.5647 (tt) REVERT: S 478 MET cc_start: 0.5218 (OUTLIER) cc_final: 0.3737 (tpt) REVERT: S 692 THR cc_start: 0.1657 (p) cc_final: 0.1145 (p) REVERT: S 738 LYS cc_start: 0.5468 (OUTLIER) cc_final: 0.4761 (tppt) REVERT: R 205 VAL cc_start: 0.5349 (p) cc_final: 0.5132 (m) REVERT: R 281 LYS cc_start: 0.3894 (mptp) cc_final: 0.3440 (mmtp) REVERT: R 409 HIS cc_start: 0.5607 (OUTLIER) cc_final: 0.5154 (p-80) outliers start: 248 outliers final: 85 residues processed: 1022 average time/residue: 1.0396 time to fit residues: 1418.5510 Evaluate side-chains 798 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 693 time to evaluate : 4.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 337 MET Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1152 SER Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 121 ASN Chi-restraints excluded: chain O residue 131 HIS Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 378 THR Chi-restraints excluded: chain Q residue 92 PHE Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 241 GLU Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain S residue 478 MET Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain S residue 738 LYS Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 157 MET Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 520 optimal weight: 20.0000 chunk 355 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 465 optimal weight: 9.9990 chunk 258 optimal weight: 0.0570 chunk 533 optimal weight: 10.0000 chunk 432 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 319 optimal weight: 0.7980 chunk 561 optimal weight: 0.9980 chunk 157 optimal weight: 0.1980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 89 GLN M 351 HIS A 344 ASN A 378 HIS ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1314 GLN B 173 ASN B 248 ASN B 295 ASN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN B 745 GLN B 896 GLN B 899 GLN D 30 HIS E 106 GLN E 136 ASN ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 131 HIS O 488 HIS Q 85 GLN S 624 GLN R 298 GLN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 54980 Z= 0.206 Angle : 0.671 14.954 74686 Z= 0.341 Chirality : 0.044 0.275 8352 Planarity : 0.005 0.091 9248 Dihedral : 13.746 179.962 8035 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.60 % Favored : 94.38 % Rotamer: Outliers : 4.27 % Allowed : 19.99 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.10), residues: 6352 helix: -0.64 (0.11), residues: 2280 sheet: -1.25 (0.18), residues: 744 loop : -1.75 (0.10), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP S 438 HIS 0.047 0.001 HIS O 131 PHE 0.031 0.002 PHE C 315 TYR 0.027 0.002 TYR S 715 ARG 0.012 0.001 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 879 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 159 ILE cc_start: 0.4260 (OUTLIER) cc_final: 0.3992 (pp) REVERT: M 166 ARG cc_start: 0.2071 (mtt90) cc_final: 0.1572 (ttt90) REVERT: A 26 ASN cc_start: 0.7564 (t0) cc_final: 0.7317 (t0) REVERT: A 59 ARG cc_start: 0.6751 (tpm170) cc_final: 0.5699 (mtp85) REVERT: A 118 TYR cc_start: 0.7004 (m-80) cc_final: 0.6716 (m-80) REVERT: A 329 ARG cc_start: 0.6017 (mmm160) cc_final: 0.5555 (tpp-160) REVERT: A 331 GLU cc_start: 0.4175 (OUTLIER) cc_final: 0.3906 (mp0) REVERT: A 585 ASP cc_start: 0.7916 (m-30) cc_final: 0.7477 (m-30) REVERT: A 662 SER cc_start: 0.7227 (p) cc_final: 0.6824 (m) REVERT: A 760 TRP cc_start: 0.6947 (m100) cc_final: 0.6675 (m100) REVERT: A 1089 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6075 (pp) REVERT: A 1099 LYS cc_start: 0.5411 (OUTLIER) cc_final: 0.5144 (mttp) REVERT: A 1178 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6336 (pt) REVERT: A 1326 GLU cc_start: 0.4709 (mt-10) cc_final: 0.4316 (pt0) REVERT: A 1513 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: A 1589 MET cc_start: 0.7330 (mmm) cc_final: 0.7121 (mmm) REVERT: A 1620 GLN cc_start: 0.7684 (tp40) cc_final: 0.7229 (tm-30) REVERT: B 411 MET cc_start: 0.4860 (ptt) cc_final: 0.4471 (ptt) REVERT: B 443 LYS cc_start: 0.6743 (tptp) cc_final: 0.6341 (tppt) REVERT: B 446 MET cc_start: 0.7446 (tmt) cc_final: 0.7058 (tmt) REVERT: B 457 ILE cc_start: 0.7857 (mm) cc_final: 0.7653 (mm) REVERT: B 460 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7157 (mppt) REVERT: B 512 LEU cc_start: 0.6499 (mt) cc_final: 0.5901 (tp) REVERT: B 611 TRP cc_start: 0.6284 (m100) cc_final: 0.5572 (m100) REVERT: B 641 TYR cc_start: 0.4498 (m-10) cc_final: 0.3896 (m-80) REVERT: B 672 MET cc_start: 0.2706 (OUTLIER) cc_final: 0.2343 (ptp) REVERT: B 787 MET cc_start: 0.6532 (ppp) cc_final: 0.6200 (pp-130) REVERT: B 915 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: B 1066 HIS cc_start: 0.5308 (t-90) cc_final: 0.4923 (m170) REVERT: B 1133 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5220 (ptm) REVERT: B 1155 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.5642 (p0) REVERT: C 264 GLU cc_start: 0.2823 (OUTLIER) cc_final: 0.2543 (pm20) REVERT: D 15 THR cc_start: 0.8266 (t) cc_final: 0.7994 (t) REVERT: E 21 GLU cc_start: 0.5745 (OUTLIER) cc_final: 0.5473 (tt0) REVERT: E 50 MET cc_start: 0.4890 (pmm) cc_final: 0.4674 (pmm) REVERT: E 93 MET cc_start: 0.6797 (tpp) cc_final: 0.6147 (tpp) REVERT: E 94 LYS cc_start: 0.7024 (mmmm) cc_final: 0.6750 (tmtt) REVERT: E 121 MET cc_start: 0.5588 (tpp) cc_final: 0.5306 (tpp) REVERT: E 123 LEU cc_start: 0.5905 (tp) cc_final: 0.5549 (tp) REVERT: G 136 TYR cc_start: 0.5640 (OUTLIER) cc_final: 0.4910 (m-80) REVERT: H 77 ARG cc_start: 0.6334 (OUTLIER) cc_final: 0.4695 (mtm110) REVERT: H 123 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6447 (ptm) REVERT: H 130 ARG cc_start: 0.5706 (ptp90) cc_final: 0.5357 (ptp90) REVERT: H 144 ILE cc_start: 0.7396 (mp) cc_final: 0.7107 (mp) REVERT: I 94 MET cc_start: 0.1526 (ttt) cc_final: 0.1113 (tmt) REVERT: K 55 SER cc_start: 0.7660 (t) cc_final: 0.7299 (p) REVERT: L 42 ARG cc_start: 0.5900 (ptp-110) cc_final: 0.5383 (mtt-85) REVERT: N 30 LYS cc_start: 0.6170 (pttt) cc_final: 0.5869 (tppt) REVERT: N 90 MET cc_start: 0.4520 (ttp) cc_final: 0.3789 (tmt) REVERT: O 123 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6529 (pp20) REVERT: O 124 LYS cc_start: 0.6502 (mmtp) cc_final: 0.5139 (mtpm) REVERT: O 156 MET cc_start: 0.5039 (ttt) cc_final: 0.4476 (mmm) REVERT: O 173 HIS cc_start: 0.3714 (t-90) cc_final: 0.3069 (t-90) REVERT: O 206 ARG cc_start: 0.6301 (mmm160) cc_final: 0.5056 (mpp-170) REVERT: O 380 SER cc_start: 0.6692 (m) cc_final: 0.6157 (t) REVERT: O 582 ARG cc_start: 0.4061 (tpt90) cc_final: 0.3525 (mtp180) REVERT: O 584 GLN cc_start: 0.5720 (tp40) cc_final: 0.3688 (mp10) REVERT: Q 74 GLN cc_start: 0.2179 (mt0) cc_final: 0.1640 (tp40) REVERT: Q 79 GLN cc_start: 0.5770 (tm130) cc_final: 0.5365 (tm-30) REVERT: Q 139 LYS cc_start: 0.5507 (tttt) cc_final: 0.5030 (tttp) REVERT: Q 240 LYS cc_start: 0.6794 (mmmt) cc_final: 0.5583 (mttp) REVERT: Q 371 GLU cc_start: 0.6877 (tp30) cc_final: 0.6549 (mm-30) REVERT: Q 421 ARG cc_start: 0.4786 (ttt180) cc_final: 0.4110 (tpm170) REVERT: S 16 LEU cc_start: 0.5024 (tt) cc_final: 0.4718 (tt) REVERT: S 45 PRO cc_start: 0.1616 (Cg_endo) cc_final: 0.1016 (Cg_exo) REVERT: S 247 ILE cc_start: 0.3629 (OUTLIER) cc_final: 0.2851 (tp) REVERT: S 285 MET cc_start: 0.4474 (ppp) cc_final: 0.3883 (tpp) REVERT: S 762 ARG cc_start: 0.5886 (mmm160) cc_final: 0.4925 (mmt90) REVERT: R 16 ARG cc_start: 0.6508 (ptp90) cc_final: 0.6184 (ptt180) REVERT: R 205 VAL cc_start: 0.5799 (p) cc_final: 0.5535 (m) REVERT: R 281 LYS cc_start: 0.4553 (mptp) cc_final: 0.3812 (mmtp) REVERT: R 409 HIS cc_start: 0.5749 (OUTLIER) cc_final: 0.5217 (p-80) outliers start: 247 outliers final: 100 residues processed: 1041 average time/residue: 1.0805 time to fit residues: 1491.8422 Evaluate side-chains 865 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 746 time to evaluate : 4.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 256 MET Chi-restraints excluded: chain M residue 337 MET Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1099 LYS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1042 ASP Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain Q residue 92 PHE Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 325 SER Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 443 ASP Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 210 optimal weight: 1.9990 chunk 563 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 chunk 367 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 625 optimal weight: 0.6980 chunk 519 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 328 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A 949 GLN A1072 ASN ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN A1503 HIS B 166 GLN B 248 ASN B 295 ASN B 896 GLN B 987 ASN ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN D 30 HIS E 136 ASN G 74 ASN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN O 117 GLN O 121 ASN ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 488 HIS Q 85 GLN Q 115 GLN Q 131 HIS Q 145 ASN Q 157 HIS S 479 HIS ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.8297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 54980 Z= 0.208 Angle : 0.675 17.436 74686 Z= 0.342 Chirality : 0.045 0.275 8352 Planarity : 0.005 0.071 9248 Dihedral : 13.731 179.716 8034 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 4.16 % Allowed : 21.90 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.10), residues: 6352 helix: -0.41 (0.11), residues: 2273 sheet: -1.18 (0.18), residues: 751 loop : -1.63 (0.10), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 842 HIS 0.016 0.001 HIS A1293 PHE 0.037 0.002 PHE S 369 TYR 0.033 0.002 TYR A1302 ARG 0.012 0.001 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 905 time to evaluate : 4.439 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: M 57 ASN cc_start: 0.4588 (p0) cc_final: 0.4358 (p0) REVERT: M 159 ILE cc_start: 0.4329 (OUTLIER) cc_final: 0.4064 (pp) REVERT: M 166 ARG cc_start: 0.1938 (mtt90) cc_final: 0.1318 (ttm-80) REVERT: M 359 LYS cc_start: 0.4574 (tptt) cc_final: 0.4052 (tptt) REVERT: A 26 ASN cc_start: 0.8045 (t0) cc_final: 0.7715 (t0) REVERT: A 184 LYS cc_start: 0.5871 (tttt) cc_final: 0.5556 (tppt) REVERT: A 329 ARG cc_start: 0.6506 (mmm160) cc_final: 0.6224 (tpt170) REVERT: A 487 ASP cc_start: 0.7867 (t0) cc_final: 0.7605 (t0) REVERT: A 578 TYR cc_start: 0.8380 (m-10) cc_final: 0.8166 (m-10) REVERT: A 585 ASP cc_start: 0.8274 (m-30) cc_final: 0.8046 (m-30) REVERT: A 589 MET cc_start: 0.8029 (mpt) cc_final: 0.6946 (mpt) REVERT: A 662 SER cc_start: 0.7951 (p) cc_final: 0.7361 (m) REVERT: A 1047 GLN cc_start: 0.7943 (mt0) cc_final: 0.7638 (mt0) REVERT: A 1063 MET cc_start: 0.6529 (mmm) cc_final: 0.6299 (mmm) REVERT: A 1170 MET cc_start: 0.7434 (mmm) cc_final: 0.7228 (mmp) REVERT: A 1178 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7110 (pt) REVERT: A 1323 HIS cc_start: 0.5666 (m170) cc_final: 0.5446 (m-70) REVERT: A 1326 GLU cc_start: 0.5059 (mt-10) cc_final: 0.4549 (pt0) REVERT: A 1486 VAL cc_start: 0.6899 (OUTLIER) cc_final: 0.6699 (p) REVERT: A 1513 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6668 (tm-30) REVERT: A 1620 GLN cc_start: 0.7780 (tp40) cc_final: 0.7122 (tm-30) REVERT: B 166 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8196 (mm-40) REVERT: B 205 MET cc_start: 0.7232 (ptp) cc_final: 0.7003 (ptt) REVERT: B 257 GLN cc_start: 0.5296 (tp40) cc_final: 0.5060 (mm-40) REVERT: B 411 MET cc_start: 0.5630 (ptt) cc_final: 0.5352 (ptt) REVERT: B 443 LYS cc_start: 0.7172 (tptp) cc_final: 0.6565 (ttmt) REVERT: B 446 MET cc_start: 0.7590 (tmt) cc_final: 0.7004 (tmm) REVERT: B 460 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7491 (mppt) REVERT: B 512 LEU cc_start: 0.6097 (mt) cc_final: 0.5564 (tp) REVERT: B 641 TYR cc_start: 0.5559 (m-80) cc_final: 0.5145 (m-80) REVERT: B 724 GLN cc_start: 0.7092 (tt0) cc_final: 0.6857 (tt0) REVERT: B 763 ASP cc_start: 0.5287 (OUTLIER) cc_final: 0.4940 (p0) REVERT: B 898 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4474 (tp) REVERT: B 1043 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6672 (ttmm) REVERT: B 1066 HIS cc_start: 0.5056 (t-90) cc_final: 0.4845 (m170) REVERT: B 1075 GLU cc_start: 0.6987 (tp30) cc_final: 0.6435 (tp30) REVERT: B 1133 MET cc_start: 0.6179 (OUTLIER) cc_final: 0.5251 (ptm) REVERT: C 93 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: C 264 GLU cc_start: 0.3114 (OUTLIER) cc_final: 0.2613 (pm20) REVERT: D 16 LEU cc_start: 0.7265 (tp) cc_final: 0.6529 (pp) REVERT: E 12 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5583 (pp) REVERT: E 93 MET cc_start: 0.6856 (tpp) cc_final: 0.6162 (tpp) REVERT: E 123 LEU cc_start: 0.6148 (tp) cc_final: 0.5836 (tp) REVERT: F 89 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: F 116 ASP cc_start: 0.7763 (t0) cc_final: 0.7548 (t0) REVERT: G 30 GLU cc_start: 0.3837 (OUTLIER) cc_final: 0.3598 (pp20) REVERT: G 84 TYR cc_start: 0.7572 (p90) cc_final: 0.7287 (p90) REVERT: G 134 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5785 (tp30) REVERT: H 77 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.4721 (mtm110) REVERT: H 123 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7012 (ttt) REVERT: H 144 ILE cc_start: 0.7845 (mp) cc_final: 0.7332 (mp) REVERT: K 55 SER cc_start: 0.7963 (t) cc_final: 0.7661 (p) REVERT: K 110 GLU cc_start: 0.7017 (pp20) cc_final: 0.6774 (pp20) REVERT: K 134 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7246 (mmtp) REVERT: L 42 ARG cc_start: 0.6172 (ptp-110) cc_final: 0.5720 (mtt-85) REVERT: N 30 LYS cc_start: 0.6149 (pttt) cc_final: 0.5911 (tppt) REVERT: N 90 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.3914 (tmt) REVERT: O 124 LYS cc_start: 0.6960 (mmtp) cc_final: 0.5511 (mtpm) REVERT: O 156 MET cc_start: 0.5081 (ttt) cc_final: 0.4689 (tpt) REVERT: O 157 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6912 (tp) REVERT: O 173 HIS cc_start: 0.3797 (t-90) cc_final: 0.2695 (t70) REVERT: O 182 MET cc_start: 0.3034 (mmp) cc_final: 0.1335 (mmp) REVERT: O 206 ARG cc_start: 0.6106 (mmm160) cc_final: 0.5784 (tpp-160) REVERT: O 526 LEU cc_start: 0.5215 (OUTLIER) cc_final: 0.4727 (pp) REVERT: O 582 ARG cc_start: 0.4119 (tpt90) cc_final: 0.3474 (mtp180) REVERT: O 584 GLN cc_start: 0.6317 (tp40) cc_final: 0.4233 (mp10) REVERT: Q 74 GLN cc_start: 0.1430 (mt0) cc_final: 0.0999 (tp40) REVERT: Q 82 GLN cc_start: 0.4105 (tp-100) cc_final: 0.3870 (tp-100) REVERT: Q 153 LYS cc_start: 0.1787 (mmmt) cc_final: 0.1436 (tppt) REVERT: Q 158 MET cc_start: 0.3097 (tpt) cc_final: 0.0985 (ptm) REVERT: Q 192 TYR cc_start: 0.3645 (t80) cc_final: 0.3213 (t80) REVERT: Q 240 LYS cc_start: 0.6303 (mmmt) cc_final: 0.5567 (mttp) REVERT: Q 241 GLU cc_start: 0.5188 (OUTLIER) cc_final: 0.4903 (pm20) REVERT: Q 303 GLU cc_start: 0.4628 (mp0) cc_final: 0.4323 (mp0) REVERT: Q 311 MET cc_start: 0.6176 (tpp) cc_final: 0.5812 (tmm) REVERT: Q 371 GLU cc_start: 0.7020 (tp30) cc_final: 0.6790 (mm-30) REVERT: Q 421 ARG cc_start: 0.5017 (ttt180) cc_final: 0.4223 (tpm170) REVERT: Q 440 GLU cc_start: 0.5544 (mp0) cc_final: 0.5323 (pm20) REVERT: S 16 LEU cc_start: 0.4886 (tt) cc_final: 0.4566 (tt) REVERT: S 21 GLN cc_start: 0.6129 (mm110) cc_final: 0.5713 (mp10) REVERT: S 45 PRO cc_start: 0.1586 (Cg_endo) cc_final: 0.1000 (Cg_exo) REVERT: S 247 ILE cc_start: 0.4001 (OUTLIER) cc_final: 0.3330 (tp) REVERT: S 285 MET cc_start: 0.4366 (ppp) cc_final: 0.3723 (tpp) REVERT: S 386 MET cc_start: 0.3712 (ttp) cc_final: 0.3197 (tmm) REVERT: S 414 ILE cc_start: 0.6208 (tp) cc_final: 0.5697 (pt) REVERT: S 421 ILE cc_start: 0.5571 (tt) cc_final: 0.5204 (tt) REVERT: S 679 LEU cc_start: 0.2905 (mm) cc_final: 0.2526 (pp) REVERT: R 16 ARG cc_start: 0.6898 (ptp90) cc_final: 0.6511 (pmm-80) REVERT: R 139 GLU cc_start: 0.6009 (mt-10) cc_final: 0.5702 (mt-10) REVERT: R 205 VAL cc_start: 0.6138 (p) cc_final: 0.5887 (m) REVERT: R 207 ASN cc_start: 0.5085 (t0) cc_final: 0.4432 (t0) REVERT: R 324 MET cc_start: 0.5432 (mpm) cc_final: 0.5152 (mpm) REVERT: R 409 HIS cc_start: 0.5606 (OUTLIER) cc_final: 0.4986 (p-80) outliers start: 241 outliers final: 98 residues processed: 1062 average time/residue: 1.0729 time to fit residues: 1515.3069 Evaluate side-chains 866 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 744 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 256 MET Chi-restraints excluded: chain M residue 337 MET Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1567 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 691 PHE Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1042 ASP Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 19 ASN Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain Q residue 241 GLU Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 498 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 404 ASP Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 410 TYR Chi-restraints excluded: chain R residue 443 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 603 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 356 optimal weight: 1.9990 chunk 457 optimal weight: 1.9990 chunk 354 optimal weight: 0.2980 chunk 526 optimal weight: 0.8980 chunk 349 optimal weight: 0.9990 chunk 623 optimal weight: 3.9990 chunk 390 optimal weight: 0.8980 chunk 380 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 16 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 553 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 HIS ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 295 ASN B 325 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B 896 GLN ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 30 HIS E 136 ASN E 146 HIS G 154 ASN H 137 GLN I 125 ASN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 131 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 488 HIS Q 85 GLN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.9236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 54980 Z= 0.235 Angle : 0.687 17.797 74686 Z= 0.348 Chirality : 0.045 0.433 8352 Planarity : 0.005 0.099 9248 Dihedral : 13.728 179.878 8030 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.62 % Favored : 94.36 % Rotamer: Outliers : 4.23 % Allowed : 23.67 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.10), residues: 6352 helix: -0.27 (0.11), residues: 2264 sheet: -1.10 (0.18), residues: 758 loop : -1.58 (0.11), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP S 438 HIS 0.012 0.001 HIS B 688 PHE 0.065 0.002 PHE B 691 TYR 0.036 0.002 TYR Q 227 ARG 0.014 0.001 ARG H 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 908 time to evaluate : 4.463 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: M 48 LYS cc_start: 0.1380 (pptt) cc_final: 0.0761 (pmtt) REVERT: M 57 ASN cc_start: 0.4804 (p0) cc_final: 0.4591 (p0) REVERT: M 159 ILE cc_start: 0.4399 (OUTLIER) cc_final: 0.4060 (pp) REVERT: M 166 ARG cc_start: 0.2149 (mtt90) cc_final: 0.1869 (ttt90) REVERT: M 359 LYS cc_start: 0.5236 (tptt) cc_final: 0.4775 (tttm) REVERT: A 26 ASN cc_start: 0.8133 (t0) cc_final: 0.7692 (t0) REVERT: A 59 ARG cc_start: 0.7017 (tpm170) cc_final: 0.5904 (mtp85) REVERT: A 120 CYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7450 (t) REVERT: A 205 ARG cc_start: 0.6705 (mtm110) cc_final: 0.6290 (ttt-90) REVERT: A 321 LYS cc_start: 0.7044 (tmmt) cc_final: 0.6631 (tppp) REVERT: A 329 ARG cc_start: 0.6909 (mmm160) cc_final: 0.6526 (tpt170) REVERT: A 439 ASP cc_start: 0.6914 (m-30) cc_final: 0.5787 (t70) REVERT: A 725 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8368 (mm) REVERT: A 917 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7623 (ptt) REVERT: A 934 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8101 (mmmt) REVERT: A 960 MET cc_start: 0.6726 (mmt) cc_final: 0.6497 (mpt) REVERT: A 1012 LYS cc_start: 0.5589 (ttpt) cc_final: 0.5258 (tppt) REVERT: A 1088 HIS cc_start: 0.8560 (m-70) cc_final: 0.8248 (m90) REVERT: A 1170 MET cc_start: 0.7882 (mmm) cc_final: 0.7637 (mmp) REVERT: A 1290 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.4521 (t80) REVERT: A 1323 HIS cc_start: 0.6142 (m170) cc_final: 0.5906 (m-70) REVERT: A 1326 GLU cc_start: 0.5342 (mt-10) cc_final: 0.4748 (pt0) REVERT: A 1444 ARG cc_start: 0.6923 (ptp-170) cc_final: 0.6669 (ptp90) REVERT: A 1485 MET cc_start: 0.7332 (mmm) cc_final: 0.6730 (tpp) REVERT: A 1490 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7065 (tt0) REVERT: A 1513 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: A 1620 GLN cc_start: 0.7957 (tp40) cc_final: 0.7466 (tm-30) REVERT: A 1621 PHE cc_start: 0.7332 (m-80) cc_final: 0.7104 (m-80) REVERT: B 16 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5302 (p90) REVERT: B 131 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7151 (p) REVERT: B 164 MET cc_start: 0.7551 (tpp) cc_final: 0.7296 (tpp) REVERT: B 411 MET cc_start: 0.6418 (ptt) cc_final: 0.6181 (ptt) REVERT: B 443 LYS cc_start: 0.7140 (tptp) cc_final: 0.6508 (tppt) REVERT: B 446 MET cc_start: 0.7766 (tmt) cc_final: 0.7174 (tmm) REVERT: B 460 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7848 (mppt) REVERT: B 512 LEU cc_start: 0.6338 (mt) cc_final: 0.5747 (tp) REVERT: B 626 ILE cc_start: 0.6053 (pt) cc_final: 0.5825 (pt) REVERT: B 898 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5049 (tp) REVERT: B 977 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7504 (pp) REVERT: B 1028 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8878 (t) REVERT: B 1066 HIS cc_start: 0.5456 (t-90) cc_final: 0.5148 (m170) REVERT: B 1155 ASP cc_start: 0.5906 (OUTLIER) cc_final: 0.5670 (p0) REVERT: D 16 LEU cc_start: 0.7330 (tp) cc_final: 0.6714 (pp) REVERT: E 22 MET cc_start: 0.8160 (ttp) cc_final: 0.7747 (ttm) REVERT: E 81 GLU cc_start: 0.6073 (tm-30) cc_final: 0.5665 (tp30) REVERT: E 93 MET cc_start: 0.7064 (tpp) cc_final: 0.6356 (tpp) REVERT: E 123 LEU cc_start: 0.6042 (tp) cc_final: 0.5820 (tp) REVERT: E 194 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6963 (mt-10) REVERT: F 89 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8699 (mt-10) REVERT: F 119 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6812 (mmt180) REVERT: G 30 GLU cc_start: 0.4301 (OUTLIER) cc_final: 0.4051 (pp20) REVERT: G 75 ASN cc_start: 0.6096 (m-40) cc_final: 0.5447 (t0) REVERT: G 134 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5767 (tp30) REVERT: G 248 THR cc_start: 0.6726 (OUTLIER) cc_final: 0.6426 (p) REVERT: H 77 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.4633 (mtm110) REVERT: H 123 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7496 (ttt) REVERT: H 126 GLU cc_start: 0.6053 (tp30) cc_final: 0.5840 (tp30) REVERT: J 67 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.6013 (pp20) REVERT: K 55 SER cc_start: 0.8203 (t) cc_final: 0.7917 (p) REVERT: K 101 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7857 (tp) REVERT: K 134 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7853 (mmtp) REVERT: L 42 ARG cc_start: 0.6237 (ptp-110) cc_final: 0.5934 (mtt-85) REVERT: L 68 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6953 (mt-10) REVERT: N 30 LYS cc_start: 0.6303 (pttt) cc_final: 0.5982 (mmtt) REVERT: N 90 MET cc_start: 0.4830 (OUTLIER) cc_final: 0.4127 (tmt) REVERT: N 169 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.6051 (mt-10) REVERT: O 124 LYS cc_start: 0.7068 (mmtp) cc_final: 0.5838 (mtpm) REVERT: O 156 MET cc_start: 0.5487 (ttt) cc_final: 0.5063 (tpt) REVERT: O 173 HIS cc_start: 0.3828 (t-90) cc_final: 0.3234 (t-90) REVERT: O 201 LYS cc_start: 0.5462 (OUTLIER) cc_final: 0.5160 (tttt) REVERT: O 206 ARG cc_start: 0.6496 (mmm160) cc_final: 0.5342 (mpp-170) REVERT: O 582 ARG cc_start: 0.4095 (tpt90) cc_final: 0.3342 (mtp180) REVERT: O 584 GLN cc_start: 0.6314 (tp40) cc_final: 0.4097 (mp10) REVERT: O 590 SER cc_start: 0.5593 (m) cc_final: 0.5046 (p) REVERT: Q 82 GLN cc_start: 0.4086 (tp-100) cc_final: 0.3867 (tp-100) REVERT: Q 139 LYS cc_start: 0.5260 (tttt) cc_final: 0.4892 (tptt) REVERT: Q 143 THR cc_start: 0.6307 (m) cc_final: 0.6101 (t) REVERT: Q 190 MET cc_start: 0.1465 (tpp) cc_final: -0.0030 (tpt) REVERT: Q 240 LYS cc_start: 0.6468 (mmmt) cc_final: 0.5812 (mttp) REVERT: Q 258 MET cc_start: 0.5501 (ptt) cc_final: 0.4753 (mmt) REVERT: Q 311 MET cc_start: 0.5924 (tpp) cc_final: 0.5479 (ttt) REVERT: Q 371 GLU cc_start: 0.7276 (tp30) cc_final: 0.7026 (mm-30) REVERT: Q 421 ARG cc_start: 0.5116 (ttt180) cc_final: 0.4202 (tpm170) REVERT: Q 440 GLU cc_start: 0.5693 (mp0) cc_final: 0.5434 (pm20) REVERT: S 16 LEU cc_start: 0.4952 (tt) cc_final: 0.4674 (tt) REVERT: S 45 PRO cc_start: 0.1739 (Cg_endo) cc_final: 0.1109 (Cg_exo) REVERT: S 247 ILE cc_start: 0.4097 (OUTLIER) cc_final: 0.3608 (tp) REVERT: S 386 MET cc_start: 0.4026 (ttp) cc_final: 0.3486 (tmm) REVERT: S 421 ILE cc_start: 0.5464 (tt) cc_final: 0.5102 (tt) REVERT: S 678 LEU cc_start: 0.6068 (mp) cc_final: 0.5653 (tp) REVERT: S 736 ILE cc_start: 0.4011 (OUTLIER) cc_final: 0.3769 (tt) REVERT: R 16 ARG cc_start: 0.6976 (ptp90) cc_final: 0.6521 (pmm-80) REVERT: R 196 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6484 (mm-30) REVERT: R 207 ASN cc_start: 0.5207 (t0) cc_final: 0.4544 (t0) REVERT: R 247 ILE cc_start: 0.5480 (OUTLIER) cc_final: 0.5031 (mp) REVERT: R 268 LEU cc_start: 0.7077 (tm) cc_final: 0.6732 (tp) REVERT: R 271 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6378 (mt) REVERT: R 274 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5969 (tpt) REVERT: R 324 MET cc_start: 0.5378 (mpm) cc_final: 0.5038 (mpm) outliers start: 245 outliers final: 101 residues processed: 1073 average time/residue: 1.1268 time to fit residues: 1609.5841 Evaluate side-chains 912 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 780 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 62 TYR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 256 MET Chi-restraints excluded: chain M residue 337 MET Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1290 TYR Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 842 GLU Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1042 ASP Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 19 ASN Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 488 HIS Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 498 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 404 ASP Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 443 ASP Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain S residue 736 ILE Chi-restraints excluded: chain S residue 738 LYS Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 408 ILE Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 385 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 372 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 396 optimal weight: 7.9990 chunk 424 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 490 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 HIS A 322 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS A 580 HIS ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1113 HIS ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1544 ASN A1567 ASN B 173 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 499 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN B 824 HIS B 867 ASN B 896 GLN ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN B1089 GLN C 88 ASN C 93 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 106 GLN G 20 HIS G 150 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS O 168 GLN O 172 HIS O 390 GLN ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 583 GLN Q 85 GLN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 1.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.270 54980 Z= 0.315 Angle : 0.812 20.167 74686 Z= 0.412 Chirality : 0.049 0.547 8352 Planarity : 0.006 0.111 9248 Dihedral : 13.895 178.442 8030 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.69 % Rotamer: Outliers : 4.11 % Allowed : 25.48 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.10), residues: 6352 helix: -0.39 (0.11), residues: 2247 sheet: -1.11 (0.19), residues: 741 loop : -1.62 (0.10), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP S 438 HIS 0.086 0.002 HIS O 488 PHE 0.035 0.002 PHE B 301 TYR 0.034 0.002 TYR B 760 ARG 0.037 0.001 ARG O 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1000 time to evaluate : 4.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 48 LYS cc_start: 0.1851 (pptt) cc_final: 0.0950 (pmtt) REVERT: M 65 TYR cc_start: 0.5594 (p90) cc_final: 0.5249 (p90) REVERT: M 95 VAL cc_start: 0.5966 (p) cc_final: 0.5604 (t) REVERT: M 159 ILE cc_start: 0.3804 (OUTLIER) cc_final: 0.3564 (pp) REVERT: M 166 ARG cc_start: 0.2880 (mtt90) cc_final: 0.2517 (mtt-85) REVERT: M 359 LYS cc_start: 0.5106 (tptt) cc_final: 0.4813 (tttm) REVERT: A 59 ARG cc_start: 0.7293 (tpm170) cc_final: 0.6296 (mtp85) REVERT: A 104 PHE cc_start: 0.6786 (m-80) cc_final: 0.6318 (m-80) REVERT: A 120 CYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7640 (t) REVERT: A 214 ASP cc_start: 0.7000 (t0) cc_final: 0.6766 (t0) REVERT: A 321 LYS cc_start: 0.7736 (tmmt) cc_final: 0.7383 (tppp) REVERT: A 355 PHE cc_start: 0.8305 (m-80) cc_final: 0.7959 (m-80) REVERT: A 512 THR cc_start: 0.8878 (m) cc_final: 0.8648 (p) REVERT: A 783 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8336 (tmmt) REVERT: A 892 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7952 (tp) REVERT: A 934 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8193 (mmmt) REVERT: A 937 ASN cc_start: 0.7559 (m-40) cc_final: 0.6872 (t160) REVERT: A 973 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5464 (tt0) REVERT: A 1000 MET cc_start: 0.8385 (mtp) cc_final: 0.7838 (mtp) REVERT: A 1047 GLN cc_start: 0.8414 (mt0) cc_final: 0.8094 (mt0) REVERT: A 1049 MET cc_start: 0.8346 (mmt) cc_final: 0.8082 (mmt) REVERT: A 1063 MET cc_start: 0.8102 (mmm) cc_final: 0.7699 (mmp) REVERT: A 1088 HIS cc_start: 0.8118 (m-70) cc_final: 0.7544 (m90) REVERT: A 1170 MET cc_start: 0.8544 (mmm) cc_final: 0.8284 (mmp) REVERT: A 1176 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7597 (mmp-170) REVERT: A 1269 LYS cc_start: 0.7147 (mtmt) cc_final: 0.6715 (mtpp) REVERT: A 1290 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.5810 (t80) REVERT: A 1326 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6110 (pt0) REVERT: A 1485 MET cc_start: 0.7835 (mmm) cc_final: 0.7429 (tpp) REVERT: A 1513 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6439 (tm-30) REVERT: A 1568 ASN cc_start: 0.8234 (m-40) cc_final: 0.7967 (m-40) REVERT: A 1583 ASP cc_start: 0.7332 (m-30) cc_final: 0.6907 (t0) REVERT: A 1620 GLN cc_start: 0.8019 (tp40) cc_final: 0.7460 (tp-100) REVERT: B 16 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.5250 (p90) REVERT: B 265 ARG cc_start: 0.7161 (tpp80) cc_final: 0.6888 (tpm170) REVERT: B 411 MET cc_start: 0.8110 (ptt) cc_final: 0.7852 (ptt) REVERT: B 443 LYS cc_start: 0.7199 (tptp) cc_final: 0.6829 (mttt) REVERT: B 446 MET cc_start: 0.8298 (tmt) cc_final: 0.7716 (tmm) REVERT: B 512 LEU cc_start: 0.7013 (mt) cc_final: 0.6352 (tp) REVERT: B 623 ASP cc_start: 0.6790 (t0) cc_final: 0.6347 (p0) REVERT: B 720 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 724 GLN cc_start: 0.7450 (tt0) cc_final: 0.7250 (mt0) REVERT: B 898 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6155 (tp) REVERT: B 977 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8333 (pt) REVERT: B 982 THR cc_start: 0.8901 (m) cc_final: 0.8631 (p) REVERT: B 1018 THR cc_start: 0.8821 (m) cc_final: 0.8591 (p) REVERT: B 1133 MET cc_start: 0.7097 (ppp) cc_final: 0.6366 (ptt) REVERT: B 1151 ILE cc_start: 0.2209 (OUTLIER) cc_final: 0.1325 (tt) REVERT: C 61 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8788 (m) REVERT: C 112 MET cc_start: 0.8233 (ttm) cc_final: 0.7952 (ttm) REVERT: D 16 LEU cc_start: 0.8196 (tp) cc_final: 0.7656 (pp) REVERT: D 29 GLN cc_start: 0.7128 (tm-30) cc_final: 0.6780 (tm-30) REVERT: D 37 LEU cc_start: 0.7260 (tt) cc_final: 0.7055 (mt) REVERT: D 45 ASP cc_start: 0.7356 (t0) cc_final: 0.7015 (t0) REVERT: E 8 ASN cc_start: 0.8545 (t0) cc_final: 0.8309 (m-40) REVERT: E 22 MET cc_start: 0.8396 (ttp) cc_final: 0.8054 (ttm) REVERT: E 50 MET cc_start: 0.5577 (pmm) cc_final: 0.4704 (ppp) REVERT: E 75 MET cc_start: 0.6938 (ptt) cc_final: 0.6720 (ptt) REVERT: E 81 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6400 (tp30) REVERT: E 93 MET cc_start: 0.7345 (tpp) cc_final: 0.6598 (tpp) REVERT: E 143 ASN cc_start: 0.8119 (t0) cc_final: 0.7704 (t0) REVERT: E 182 ASP cc_start: 0.8310 (t0) cc_final: 0.8097 (t70) REVERT: F 76 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8018 (tttt) REVERT: F 119 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7139 (mmt180) REVERT: G 59 GLN cc_start: 0.7771 (mp10) cc_final: 0.7550 (mm-40) REVERT: G 134 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5867 (tp30) REVERT: G 159 LYS cc_start: 0.6773 (mtmt) cc_final: 0.6489 (mtmt) REVERT: G 248 THR cc_start: 0.6603 (m) cc_final: 0.6382 (p) REVERT: H 37 LYS cc_start: 0.8266 (ptmt) cc_final: 0.7973 (pttm) REVERT: H 77 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6431 (ptt90) REVERT: H 100 THR cc_start: 0.8827 (p) cc_final: 0.8554 (t) REVERT: H 132 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4760 (pt) REVERT: I 64 LYS cc_start: 0.6518 (mmtp) cc_final: 0.5917 (mmtp) REVERT: I 94 MET cc_start: 0.2510 (OUTLIER) cc_final: 0.2305 (tpp) REVERT: J 67 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6547 (pp20) REVERT: K 60 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8432 (p) REVERT: K 103 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (mt) REVERT: K 122 LYS cc_start: 0.7939 (tttt) cc_final: 0.7644 (tptp) REVERT: K 134 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8407 (tppp) REVERT: L 42 ARG cc_start: 0.6540 (ptp-110) cc_final: 0.6301 (mtt-85) REVERT: N 90 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.4852 (tmm) REVERT: O 124 LYS cc_start: 0.7320 (mmtp) cc_final: 0.6024 (mtpm) REVERT: O 156 MET cc_start: 0.6021 (ttt) cc_final: 0.5597 (mmm) REVERT: O 173 HIS cc_start: 0.4622 (t-90) cc_final: 0.3568 (t-90) REVERT: O 187 MET cc_start: 0.6543 (mtp) cc_final: 0.6291 (mtm) REVERT: O 196 LYS cc_start: 0.5123 (tttt) cc_final: 0.4794 (ttmm) REVERT: O 206 ARG cc_start: 0.6529 (mmm160) cc_final: 0.5536 (mpp80) REVERT: O 242 VAL cc_start: 0.6193 (t) cc_final: 0.5902 (m) REVERT: O 243 GLU cc_start: 0.6290 (mt-10) cc_final: 0.5568 (tp30) REVERT: O 356 GLU cc_start: 0.6267 (mt-10) cc_final: 0.5851 (tm-30) REVERT: O 408 PHE cc_start: 0.5708 (m-80) cc_final: 0.5466 (m-80) REVERT: O 416 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6619 (tppt) REVERT: O 426 SER cc_start: 0.6677 (t) cc_final: 0.5741 (m) REVERT: O 522 GLU cc_start: 0.4676 (tt0) cc_final: 0.4366 (mm-30) REVERT: O 582 ARG cc_start: 0.4378 (tpt90) cc_final: 0.3200 (mtp180) REVERT: O 584 GLN cc_start: 0.6244 (tp40) cc_final: 0.4060 (mp10) REVERT: O 606 MET cc_start: 0.3809 (mmm) cc_final: 0.3482 (mmm) REVERT: Q 82 GLN cc_start: 0.4105 (tp-100) cc_final: 0.3829 (tp-100) REVERT: Q 158 MET cc_start: 0.5036 (OUTLIER) cc_final: 0.1383 (ptp) REVERT: Q 177 TYR cc_start: 0.4652 (m-80) cc_final: 0.4373 (m-80) REVERT: Q 190 MET cc_start: 0.2667 (tpp) cc_final: 0.1253 (tpt) REVERT: Q 240 LYS cc_start: 0.6339 (mmmt) cc_final: 0.5935 (mttp) REVERT: Q 292 GLU cc_start: 0.2661 (pm20) cc_final: 0.2067 (tt0) REVERT: Q 415 LYS cc_start: 0.8011 (tptt) cc_final: 0.7782 (ttmt) REVERT: Q 421 ARG cc_start: 0.5333 (ttt180) cc_final: 0.4629 (pmt170) REVERT: Q 440 GLU cc_start: 0.5916 (mp0) cc_final: 0.5685 (pm20) REVERT: S 247 ILE cc_start: 0.5298 (OUTLIER) cc_final: 0.4736 (tp) REVERT: S 285 MET cc_start: 0.3869 (ppp) cc_final: 0.3313 (tpp) REVERT: S 412 ASN cc_start: 0.4386 (t0) cc_final: 0.3679 (p0) REVERT: S 414 ILE cc_start: 0.6143 (tp) cc_final: 0.5360 (pt) REVERT: S 736 ILE cc_start: 0.3967 (mt) cc_final: 0.3745 (tt) REVERT: R 23 TYR cc_start: 0.5947 (t80) cc_final: 0.5680 (t80) REVERT: R 196 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6640 (mm-30) REVERT: R 207 ASN cc_start: 0.6021 (t0) cc_final: 0.5184 (t0) REVERT: R 271 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7247 (mt) REVERT: R 324 MET cc_start: 0.5010 (mpm) cc_final: 0.4745 (mpm) REVERT: R 359 MET cc_start: 0.3843 (pmm) cc_final: 0.3608 (ptp) outliers start: 238 outliers final: 93 residues processed: 1151 average time/residue: 1.1493 time to fit residues: 1727.0775 Evaluate side-chains 892 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 773 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 62 TYR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 256 MET Chi-restraints excluded: chain M residue 337 MET Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1290 TYR Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1066 HIS Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 94 MET Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 416 LYS Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 498 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 323 ASN Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 443 ASP Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 495 SER Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain S residue 738 LYS Chi-restraints excluded: chain S residue 765 SER Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 567 optimal weight: 10.0000 chunk 597 optimal weight: 0.9990 chunk 545 optimal weight: 0.8980 chunk 581 optimal weight: 0.5980 chunk 349 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 456 optimal weight: 0.3980 chunk 178 optimal weight: 0.9980 chunk 525 optimal weight: 0.9980 chunk 549 optimal weight: 6.9990 chunk 579 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 382 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN A 863 ASN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 HIS ** B 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN B 824 HIS B 886 ASN B 896 GLN ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN E 136 ASN G 20 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN O 131 HIS O 391 GLN O 422 GLN ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 488 HIS Q 74 GLN Q 85 GLN ** R 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 1.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 54980 Z= 0.219 Angle : 0.716 19.100 74686 Z= 0.357 Chirality : 0.046 0.275 8352 Planarity : 0.005 0.088 9248 Dihedral : 13.750 179.529 8030 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 3.09 % Allowed : 28.76 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.10), residues: 6352 helix: -0.20 (0.11), residues: 2248 sheet: -0.97 (0.19), residues: 744 loop : -1.58 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP O 125 HIS 0.039 0.001 HIS B1066 PHE 0.043 0.002 PHE B 301 TYR 0.045 0.002 TYR A 95 ARG 0.020 0.001 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 842 time to evaluate : 4.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 48 LYS cc_start: 0.1447 (pptt) cc_final: 0.0968 (pmtt) REVERT: M 65 TYR cc_start: 0.5826 (p90) cc_final: 0.5454 (p90) REVERT: M 95 VAL cc_start: 0.6100 (p) cc_final: 0.5736 (t) REVERT: M 119 THR cc_start: 0.3098 (m) cc_final: 0.2807 (p) REVERT: M 166 ARG cc_start: 0.2572 (mtt90) cc_final: 0.2180 (mtt-85) REVERT: M 359 LYS cc_start: 0.5294 (tptt) cc_final: 0.5022 (tttm) REVERT: A 59 ARG cc_start: 0.7136 (tpm170) cc_final: 0.6385 (mtp85) REVERT: A 104 PHE cc_start: 0.6716 (m-80) cc_final: 0.6489 (m-80) REVERT: A 114 GLU cc_start: 0.7903 (tp30) cc_final: 0.7419 (mm-30) REVERT: A 120 CYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7723 (t) REVERT: A 214 ASP cc_start: 0.7079 (t0) cc_final: 0.6869 (t0) REVERT: A 238 MET cc_start: 0.3574 (OUTLIER) cc_final: 0.2850 (mpp) REVERT: A 321 LYS cc_start: 0.7964 (tmmt) cc_final: 0.7435 (tppp) REVERT: A 355 PHE cc_start: 0.8335 (m-80) cc_final: 0.7976 (m-80) REVERT: A 363 PRO cc_start: 0.8682 (Cg_exo) cc_final: 0.8453 (Cg_endo) REVERT: A 574 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8130 (p0) REVERT: A 783 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8260 (tmmt) REVERT: A 892 LEU cc_start: 0.8357 (tm) cc_final: 0.7735 (tp) REVERT: A 934 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8312 (mmmt) REVERT: A 961 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8464 (m) REVERT: A 1063 MET cc_start: 0.8148 (mmm) cc_final: 0.7781 (mmp) REVERT: A 1088 HIS cc_start: 0.8011 (m-70) cc_final: 0.7546 (m170) REVERT: A 1138 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7156 (mm-30) REVERT: A 1170 MET cc_start: 0.8448 (mmm) cc_final: 0.8182 (mmp) REVERT: A 1176 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7686 (mmp-170) REVERT: A 1223 ARG cc_start: 0.7260 (mmm160) cc_final: 0.6935 (ttm170) REVERT: A 1269 LYS cc_start: 0.7323 (mtmt) cc_final: 0.6819 (mtpp) REVERT: A 1290 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.5577 (t80) REVERT: A 1323 HIS cc_start: 0.7180 (m170) cc_final: 0.6717 (m-70) REVERT: A 1326 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6134 (pt0) REVERT: A 1513 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6242 (tm-30) REVERT: A 1568 ASN cc_start: 0.8198 (m-40) cc_final: 0.7899 (m-40) REVERT: A 1583 ASP cc_start: 0.7449 (m-30) cc_final: 0.6918 (t70) REVERT: A 1620 GLN cc_start: 0.8003 (tp40) cc_final: 0.7479 (tp-100) REVERT: B 16 PHE cc_start: 0.6956 (OUTLIER) cc_final: 0.5439 (p90) REVERT: B 295 ASN cc_start: 0.6108 (m-40) cc_final: 0.5883 (m-40) REVERT: B 443 LYS cc_start: 0.7294 (tptp) cc_final: 0.6703 (mttm) REVERT: B 600 GLN cc_start: 0.7797 (tp40) cc_final: 0.7490 (tp40) REVERT: B 720 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7513 (tm-30) REVERT: B 724 GLN cc_start: 0.7444 (tt0) cc_final: 0.7225 (mt0) REVERT: B 898 LEU cc_start: 0.6816 (pt) cc_final: 0.6269 (tp) REVERT: B 977 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8342 (pt) REVERT: B 1018 THR cc_start: 0.8772 (m) cc_final: 0.8423 (p) REVERT: B 1110 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7926 (pt) REVERT: B 1133 MET cc_start: 0.6939 (ppp) cc_final: 0.6482 (ptp) REVERT: B 1198 TYR cc_start: 0.8447 (m-80) cc_final: 0.7649 (m-80) REVERT: C 112 MET cc_start: 0.8410 (ttm) cc_final: 0.8201 (ttm) REVERT: D 16 LEU cc_start: 0.8102 (tp) cc_final: 0.7766 (pp) REVERT: D 29 GLN cc_start: 0.7166 (tm-30) cc_final: 0.6867 (tm-30) REVERT: D 37 LEU cc_start: 0.7761 (tt) cc_final: 0.7509 (mp) REVERT: D 45 ASP cc_start: 0.7373 (t0) cc_final: 0.7069 (t0) REVERT: E 8 ASN cc_start: 0.8651 (t0) cc_final: 0.8369 (m-40) REVERT: E 81 GLU cc_start: 0.6714 (tm-30) cc_final: 0.6413 (tp30) REVERT: E 143 ASN cc_start: 0.8131 (t0) cc_final: 0.7883 (t0) REVERT: F 76 LYS cc_start: 0.8291 (ttmm) cc_final: 0.8001 (tttt) REVERT: F 87 LYS cc_start: 0.7044 (tttt) cc_final: 0.6820 (tttp) REVERT: F 119 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7189 (mmt180) REVERT: G 59 GLN cc_start: 0.7734 (mp10) cc_final: 0.7480 (mm-40) REVERT: G 63 LYS cc_start: 0.8587 (mptm) cc_final: 0.8308 (mtpt) REVERT: G 74 ASN cc_start: 0.7126 (OUTLIER) cc_final: 0.6835 (m-40) REVERT: G 134 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5866 (tp30) REVERT: G 248 THR cc_start: 0.6575 (m) cc_final: 0.6333 (p) REVERT: H 37 LYS cc_start: 0.8428 (ptmt) cc_final: 0.8188 (pttm) REVERT: H 77 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6411 (ptt90) REVERT: I 64 LYS cc_start: 0.6436 (mmtp) cc_final: 0.5912 (mmmm) REVERT: I 68 LYS cc_start: 0.4983 (ttpp) cc_final: 0.4313 (ptmt) REVERT: I 94 MET cc_start: 0.2478 (tmt) cc_final: 0.1564 (tmt) REVERT: J 58 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8069 (mm-30) REVERT: K 60 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8481 (p) REVERT: K 122 LYS cc_start: 0.7757 (tttt) cc_final: 0.7530 (tptp) REVERT: K 134 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8383 (tppp) REVERT: L 30 ILE cc_start: 0.8950 (mm) cc_final: 0.8382 (mm) REVERT: N 90 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.4825 (tmm) REVERT: O 124 LYS cc_start: 0.7009 (mmtp) cc_final: 0.5829 (mtpm) REVERT: O 147 ILE cc_start: 0.7545 (mt) cc_final: 0.7132 (pp) REVERT: O 156 MET cc_start: 0.6093 (ttt) cc_final: 0.5629 (tpt) REVERT: O 187 MET cc_start: 0.6642 (mtp) cc_final: 0.5984 (mmt) REVERT: O 196 LYS cc_start: 0.5262 (tttt) cc_final: 0.3904 (tptt) REVERT: O 206 ARG cc_start: 0.6388 (mmm160) cc_final: 0.6045 (tpp-160) REVERT: O 243 GLU cc_start: 0.6403 (mt-10) cc_final: 0.5826 (tp30) REVERT: O 408 PHE cc_start: 0.5815 (m-80) cc_final: 0.5563 (m-80) REVERT: O 426 SER cc_start: 0.6797 (t) cc_final: 0.5905 (m) REVERT: O 522 GLU cc_start: 0.4662 (tt0) cc_final: 0.4370 (mm-30) REVERT: O 582 ARG cc_start: 0.4459 (tpt90) cc_final: 0.3325 (mtp180) REVERT: O 584 GLN cc_start: 0.6181 (tp40) cc_final: 0.4072 (mp10) REVERT: Q 139 LYS cc_start: 0.5485 (tttt) cc_final: 0.5124 (tptt) REVERT: Q 158 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.1748 (ptm) REVERT: Q 177 TYR cc_start: 0.4577 (m-80) cc_final: 0.4147 (m-80) REVERT: Q 183 LYS cc_start: 0.5707 (ttpp) cc_final: 0.5262 (tptp) REVERT: Q 190 MET cc_start: 0.3304 (tpp) cc_final: 0.2173 (tpt) REVERT: Q 240 LYS cc_start: 0.6306 (mmmt) cc_final: 0.5821 (mttp) REVERT: Q 258 MET cc_start: 0.5750 (ptt) cc_final: 0.5002 (mmt) REVERT: Q 292 GLU cc_start: 0.2682 (pm20) cc_final: 0.2078 (tt0) REVERT: Q 306 VAL cc_start: 0.3823 (m) cc_final: 0.3328 (t) REVERT: Q 311 MET cc_start: 0.4257 (mmm) cc_final: 0.4017 (ttt) REVERT: Q 415 LYS cc_start: 0.8049 (tptt) cc_final: 0.7801 (ttmt) REVERT: S 16 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5604 (tp) REVERT: S 285 MET cc_start: 0.3948 (ppp) cc_final: 0.3405 (tpp) REVERT: S 380 MET cc_start: 0.5360 (ptp) cc_final: 0.4953 (ptm) REVERT: S 412 ASN cc_start: 0.4208 (t0) cc_final: 0.3613 (p0) REVERT: S 678 LEU cc_start: 0.6088 (mp) cc_final: 0.5559 (tm) REVERT: R 29 ARG cc_start: 0.5773 (mmm-85) cc_final: 0.5519 (tpt90) REVERT: R 196 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6657 (mm-30) REVERT: R 207 ASN cc_start: 0.6249 (t0) cc_final: 0.5390 (t0) REVERT: R 271 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7588 (mt) REVERT: R 274 MET cc_start: 0.7455 (mmp) cc_final: 0.7222 (tpt) REVERT: R 324 MET cc_start: 0.4809 (mpm) cc_final: 0.4602 (mpm) REVERT: R 346 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6545 (tp) REVERT: R 359 MET cc_start: 0.3875 (pmm) cc_final: 0.3631 (ptp) outliers start: 179 outliers final: 71 residues processed: 964 average time/residue: 1.1665 time to fit residues: 1470.4773 Evaluate side-chains 818 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 725 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 256 MET Chi-restraints excluded: chain M residue 337 MET Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1290 TYR Chi-restraints excluded: chain A residue 1492 ILE Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 611 TRP Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain I residue 19 ASN Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain O residue 171 CYS Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 85 GLN Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 498 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 323 ASN Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 443 ASP Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 630 LEU Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain S residue 738 LYS Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 381 optimal weight: 1.9990 chunk 614 optimal weight: 4.9990 chunk 375 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 427 optimal weight: 0.6980 chunk 644 optimal weight: 0.7980 chunk 593 optimal weight: 9.9990 chunk 513 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 396 optimal weight: 0.9980 chunk 314 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 82 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1047 GLN A1072 ASN ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 209 GLN B 235 GLN ** B 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B 867 ASN B 886 ASN B 896 GLN ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 HIS ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 20 HIS G 59 GLN L 53 HIS O 131 HIS O 438 GLN O 478 GLN O 488 HIS Q 74 GLN Q 115 GLN Q 434 HIS R 263 ASN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 1.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54980 Z= 0.212 Angle : 0.717 18.759 74686 Z= 0.357 Chirality : 0.045 0.281 8352 Planarity : 0.005 0.068 9248 Dihedral : 13.705 179.553 8029 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 2.40 % Allowed : 30.23 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.10), residues: 6352 helix: -0.09 (0.11), residues: 2258 sheet: -0.90 (0.19), residues: 725 loop : -1.55 (0.11), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP O 125 HIS 0.013 0.001 HIS A 571 PHE 0.035 0.002 PHE G 16 TYR 0.043 0.002 TYR A 95 ARG 0.015 0.001 ARG B 634 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 820 time to evaluate : 4.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 65 TYR cc_start: 0.5936 (p90) cc_final: 0.5549 (p90) REVERT: M 166 ARG cc_start: 0.2578 (mtt90) cc_final: 0.2232 (mmm160) REVERT: M 359 LYS cc_start: 0.5254 (tptt) cc_final: 0.5021 (tttm) REVERT: A 59 ARG cc_start: 0.7145 (tpm170) cc_final: 0.6566 (mtp85) REVERT: A 120 CYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7726 (t) REVERT: A 180 GLU cc_start: 0.6192 (pt0) cc_final: 0.5936 (pm20) REVERT: A 209 THR cc_start: 0.8507 (m) cc_final: 0.8222 (p) REVERT: A 238 MET cc_start: 0.3793 (OUTLIER) cc_final: 0.3064 (mpp) REVERT: A 321 LYS cc_start: 0.7854 (tmmt) cc_final: 0.7400 (tppp) REVERT: A 348 LYS cc_start: 0.7409 (mtmm) cc_final: 0.6718 (mptt) REVERT: A 355 PHE cc_start: 0.8566 (m-80) cc_final: 0.8255 (m-80) REVERT: A 892 LEU cc_start: 0.8399 (tm) cc_final: 0.7833 (tp) REVERT: A 934 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8430 (mmmt) REVERT: A 960 MET cc_start: 0.8220 (mmt) cc_final: 0.7986 (mpt) REVERT: A 961 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8578 (m) REVERT: A 1057 ILE cc_start: 0.8610 (mm) cc_final: 0.8333 (mm) REVERT: A 1063 MET cc_start: 0.8062 (mmm) cc_final: 0.7833 (mmp) REVERT: A 1088 HIS cc_start: 0.7847 (m-70) cc_final: 0.7517 (m170) REVERT: A 1138 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: A 1170 MET cc_start: 0.8456 (mmm) cc_final: 0.8162 (mmp) REVERT: A 1176 ARG cc_start: 0.7913 (mmm160) cc_final: 0.7642 (mmp-170) REVERT: A 1223 ARG cc_start: 0.7347 (mmm160) cc_final: 0.7133 (ttm170) REVERT: A 1269 LYS cc_start: 0.7560 (mtmt) cc_final: 0.7065 (mtpp) REVERT: A 1290 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.5546 (t80) REVERT: A 1306 TYR cc_start: 0.6347 (m-80) cc_final: 0.5567 (m-80) REVERT: A 1323 HIS cc_start: 0.6988 (m170) cc_final: 0.6510 (m-70) REVERT: A 1326 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6181 (pt0) REVERT: A 1485 MET cc_start: 0.7449 (tpp) cc_final: 0.6867 (tpt) REVERT: A 1513 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6300 (tm-30) REVERT: A 1583 ASP cc_start: 0.7437 (m-30) cc_final: 0.6919 (t70) REVERT: A 1589 MET cc_start: 0.8498 (mmm) cc_final: 0.8108 (mpp) REVERT: A 1620 GLN cc_start: 0.7981 (tp40) cc_final: 0.7554 (tm-30) REVERT: A 1655 ASP cc_start: 0.8103 (t0) cc_final: 0.7827 (m-30) REVERT: B 16 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.5460 (p90) REVERT: B 265 ARG cc_start: 0.7416 (tpm170) cc_final: 0.6703 (mmm-85) REVERT: B 443 LYS cc_start: 0.7288 (tptp) cc_final: 0.6770 (mttt) REVERT: B 446 MET cc_start: 0.7376 (tmt) cc_final: 0.6882 (tmm) REVERT: B 599 GLU cc_start: 0.7280 (mp0) cc_final: 0.7035 (mp0) REVERT: B 600 GLN cc_start: 0.7857 (tp40) cc_final: 0.7557 (tp-100) REVERT: B 720 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7444 (tm-30) REVERT: B 898 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6473 (tp) REVERT: B 900 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8537 (m) REVERT: B 977 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8407 (pt) REVERT: B 1018 THR cc_start: 0.8718 (m) cc_final: 0.8394 (p) REVERT: B 1110 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8018 (pt) REVERT: B 1198 TYR cc_start: 0.8519 (m-80) cc_final: 0.7665 (m-80) REVERT: D 16 LEU cc_start: 0.8120 (tp) cc_final: 0.7793 (pp) REVERT: D 37 LEU cc_start: 0.7784 (tt) cc_final: 0.7566 (mp) REVERT: D 45 ASP cc_start: 0.7438 (t0) cc_final: 0.7157 (t0) REVERT: D 48 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5764 (mt-10) REVERT: E 8 ASN cc_start: 0.8639 (t0) cc_final: 0.8419 (m-40) REVERT: E 11 ARG cc_start: 0.8045 (ttt-90) cc_final: 0.7822 (ttt-90) REVERT: E 50 MET cc_start: 0.5122 (pmm) cc_final: 0.4700 (ppp) REVERT: E 65 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8273 (t) REVERT: E 81 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6630 (tp30) REVERT: E 122 LYS cc_start: 0.6907 (mmmt) cc_final: 0.6506 (mmtt) REVERT: E 143 ASN cc_start: 0.8129 (t0) cc_final: 0.7844 (t0) REVERT: E 172 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7126 (mp0) REVERT: F 76 LYS cc_start: 0.8366 (ttmm) cc_final: 0.8067 (tttt) REVERT: F 87 LYS cc_start: 0.7099 (tttt) cc_final: 0.6866 (tttp) REVERT: F 119 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7222 (mmt180) REVERT: G 59 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7392 (mm-40) REVERT: G 63 LYS cc_start: 0.8610 (mptm) cc_final: 0.8314 (mtpt) REVERT: G 74 ASN cc_start: 0.7305 (m110) cc_final: 0.7069 (m-40) REVERT: G 95 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6628 (pp) REVERT: G 122 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7655 (mp) REVERT: G 134 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5810 (tp30) REVERT: G 169 VAL cc_start: 0.4013 (OUTLIER) cc_final: 0.3761 (p) REVERT: G 248 THR cc_start: 0.6454 (m) cc_final: 0.6184 (p) REVERT: H 37 LYS cc_start: 0.8553 (ptmt) cc_final: 0.8293 (pttp) REVERT: H 77 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6401 (ptt90) REVERT: I 32 GLN cc_start: 0.6649 (mp10) cc_final: 0.6446 (mp10) REVERT: I 64 LYS cc_start: 0.6894 (mmtp) cc_final: 0.6278 (mmtp) REVERT: I 68 LYS cc_start: 0.5215 (ttpp) cc_final: 0.4624 (ptpt) REVERT: I 94 MET cc_start: 0.2509 (OUTLIER) cc_final: 0.1707 (tmt) REVERT: K 60 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8493 (p) REVERT: K 134 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8325 (tppp) REVERT: L 30 ILE cc_start: 0.9022 (mm) cc_final: 0.8432 (mm) REVERT: N 90 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5033 (tmm) REVERT: O 124 LYS cc_start: 0.7142 (mmtp) cc_final: 0.5981 (mtpm) REVERT: O 147 ILE cc_start: 0.7600 (mt) cc_final: 0.7162 (pp) REVERT: O 156 MET cc_start: 0.6054 (ttt) cc_final: 0.5657 (tpt) REVERT: O 173 HIS cc_start: 0.4337 (t-90) cc_final: 0.3574 (t-90) REVERT: O 187 MET cc_start: 0.6539 (mtp) cc_final: 0.5960 (mmt) REVERT: O 196 LYS cc_start: 0.5511 (tttt) cc_final: 0.4147 (tptt) REVERT: O 206 ARG cc_start: 0.6378 (mmm160) cc_final: 0.5693 (mpp80) REVERT: O 243 GLU cc_start: 0.6547 (mt-10) cc_final: 0.5875 (tp30) REVERT: O 356 GLU cc_start: 0.6259 (mt-10) cc_final: 0.5853 (tm-30) REVERT: O 385 MET cc_start: 0.7340 (tpt) cc_final: 0.6188 (tmm) REVERT: O 423 TYR cc_start: 0.6585 (m-80) cc_final: 0.6340 (t80) REVERT: O 478 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.6080 (tm-30) REVERT: O 522 GLU cc_start: 0.4692 (tt0) cc_final: 0.4425 (mm-30) REVERT: O 582 ARG cc_start: 0.4495 (tpt90) cc_final: 0.3343 (mtp180) REVERT: O 584 GLN cc_start: 0.6100 (tp40) cc_final: 0.3968 (mp10) REVERT: Q 9 ILE cc_start: 0.7044 (tt) cc_final: 0.6650 (pp) REVERT: Q 40 GLU cc_start: 0.5434 (mm-30) cc_final: 0.5206 (tp30) REVERT: Q 177 TYR cc_start: 0.4725 (m-80) cc_final: 0.4334 (m-80) REVERT: Q 183 LYS cc_start: 0.6108 (ttpp) cc_final: 0.5497 (tptp) REVERT: Q 190 MET cc_start: 0.4016 (tpp) cc_final: 0.2619 (OUTLIER) REVERT: Q 240 LYS cc_start: 0.6322 (mmmt) cc_final: 0.5832 (mttp) REVERT: Q 258 MET cc_start: 0.5759 (ptt) cc_final: 0.5047 (mmt) REVERT: Q 292 GLU cc_start: 0.2655 (pm20) cc_final: 0.2067 (tt0) REVERT: Q 415 LYS cc_start: 0.8147 (tptt) cc_final: 0.7848 (ttmt) REVERT: Q 440 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5930 (pm20) REVERT: S 380 MET cc_start: 0.5260 (ptp) cc_final: 0.4835 (ptm) REVERT: S 412 ASN cc_start: 0.4294 (t0) cc_final: 0.3752 (p0) REVERT: S 414 ILE cc_start: 0.6257 (tp) cc_final: 0.5401 (pt) REVERT: S 678 LEU cc_start: 0.6175 (mp) cc_final: 0.5640 (tm) REVERT: R 28 SER cc_start: 0.6212 (OUTLIER) cc_final: 0.5786 (t) REVERT: R 29 ARG cc_start: 0.5792 (mmm-85) cc_final: 0.5431 (tpt90) REVERT: R 196 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6640 (mm-30) REVERT: R 271 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7794 (mt) REVERT: R 346 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6544 (tp) REVERT: R 359 MET cc_start: 0.3923 (pmm) cc_final: 0.3576 (ptp) outliers start: 139 outliers final: 66 residues processed: 915 average time/residue: 1.1733 time to fit residues: 1402.1161 Evaluate side-chains 827 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 734 time to evaluate : 4.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 256 MET Chi-restraints excluded: chain M residue 337 MET Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1290 TYR Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 41 GLN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 94 MET Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain O residue 478 GLN Chi-restraints excluded: chain O residue 488 HIS Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 440 GLU Chi-restraints excluded: chain Q residue 498 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 421 ILE Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 443 ASP Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 630 LEU Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain S residue 738 LYS Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 407 optimal weight: 3.9990 chunk 546 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 473 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 514 optimal weight: 0.0370 chunk 215 optimal weight: 5.9990 chunk 527 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 82 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1072 ASN B 166 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B 867 ASN B 896 GLN ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN G 20 HIS H 43 ASN O 131 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 488 HIS Q 74 GLN Q 85 GLN Q 87 GLN Q 115 GLN R 263 ASN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.207114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.166541 restraints weight = 73630.924| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.18 r_work: 0.3686 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 666 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 667 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 1.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 54980 Z= 0.209 Angle : 0.721 19.119 74686 Z= 0.357 Chirality : 0.045 0.280 8352 Planarity : 0.004 0.069 9248 Dihedral : 13.668 179.791 8029 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.65 % Favored : 94.33 % Rotamer: Outliers : 2.42 % Allowed : 30.73 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.10), residues: 6352 helix: -0.04 (0.11), residues: 2244 sheet: -0.86 (0.19), residues: 755 loop : -1.53 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP O 125 HIS 0.012 0.001 HIS A 571 PHE 0.043 0.002 PHE B 301 TYR 0.022 0.002 TYR A1114 ARG 0.014 0.001 ARG B 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20535.81 seconds wall clock time: 356 minutes 31.76 seconds (21391.76 seconds total)