Starting phenix.real_space_refine on Sat Feb 7 00:11:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sw0_55292/02_2026/9sw0_55292.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sw0_55292/02_2026/9sw0_55292.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/cci-nas-00/data/ceres_data/9sw0_55292/02_2026/9sw0_55292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sw0_55292/02_2026/9sw0_55292.map" model { file = "/net/cci-nas-00/data/ceres_data/9sw0_55292/02_2026/9sw0_55292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sw0_55292/02_2026/9sw0_55292.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 P 122 5.49 5 Mg 8 5.21 5 S 147 5.16 5 C 17540 2.51 5 N 5019 2.21 5 O 5679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28522 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2357 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 7, 'TRANS': 307} Chain: "F" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "G" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "M" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 551 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "N" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 716 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain: "O" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 694 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain: "E" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "A" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1924 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Chain: "C" Number of atoms: 2550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2550 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 11, 'TRANS': 312} Chain breaks: 1 Chain: "D" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2623 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 318} Chain breaks: 1 Chain: "H" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "I" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "J" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "K" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.16, per 1000 atoms: 0.25 Number of scatterers: 28522 At special positions: 0 Unit cell: (119.7, 123.5, 243.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 S 147 16.00 P 122 15.00 Mg 8 11.99 O 5679 8.00 N 5019 7.00 C 17540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6280 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 26 sheets defined 50.5% alpha, 16.1% beta 29 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'B' and resid 13 through 23 removed outlier: 3.588A pdb=" N ILE B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 46 through 62 Processing helix chain 'B' and resid 68 through 79 removed outlier: 3.796A pdb=" N THR B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.874A pdb=" N LEU B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 Processing helix chain 'B' and resid 142 through 152 removed outlier: 3.568A pdb=" N LEU B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.714A pdb=" N ARG B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 192 Processing helix chain 'B' and resid 207 through 213 removed outlier: 4.307A pdb=" N VAL B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 221 through 241 Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.702A pdb=" N PHE B 270 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 removed outlier: 4.723A pdb=" N GLU F 29 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN F 30 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 45 Processing helix chain 'F' and resid 48 through 55 Processing helix chain 'F' and resid 56 through 62 Processing helix chain 'F' and resid 67 through 82 Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 106 through 114 Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 179 removed outlier: 4.043A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 188 Processing helix chain 'F' and resid 196 through 214 removed outlier: 4.312A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER F 208 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.589A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 237 through 260 Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'G' and resid 24 through 29 Processing helix chain 'G' and resid 34 through 44 Processing helix chain 'G' and resid 48 through 55 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.886A pdb=" N ILE G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 80 Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 144 removed outlier: 3.619A pdb=" N ILE G 136 " --> pdb=" O GLY G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 178 removed outlier: 3.912A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 187 removed outlier: 3.633A pdb=" N ASP G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.965A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.687A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.550A pdb=" N LEU E 28 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU E 29 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.805A pdb=" N TYR E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 88 through 96 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 133 through 144 removed outlier: 3.726A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.693A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 removed outlier: 3.615A pdb=" N LEU E 186 " --> pdb=" O GLY E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 214 removed outlier: 4.031A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER E 214 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.558A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 288 through 296 removed outlier: 4.043A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.718A pdb=" N LEU A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 140 Processing helix chain 'A' and resid 150 through 154 removed outlier: 4.246A pdb=" N PHE A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 4.063A pdb=" N GLY A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.697A pdb=" N TYR A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.533A pdb=" N TRP A 231 " --> pdb=" O CYS A 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 34 through 39 removed outlier: 3.743A pdb=" N LEU C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 67 removed outlier: 3.671A pdb=" N GLU C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 165 through 188 removed outlier: 3.604A pdb=" N VAL C 169 " --> pdb=" O MET C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 195 removed outlier: 3.571A pdb=" N ALA C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 206 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.918A pdb=" N PHE C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 277 Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.991A pdb=" N HIS C 307 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.770A pdb=" N LEU D 5 " --> pdb=" O ASP D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 23 through 30 removed outlier: 3.556A pdb=" N PHE D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 40 Processing helix chain 'D' and resid 42 through 58 Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.735A pdb=" N LEU D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 removed outlier: 3.952A pdb=" N HIS D 79 " --> pdb=" O PHE D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 94 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 125 through 126 No H-bonds generated for 'chain 'D' and resid 125 through 126' Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 147 through 162 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 204 removed outlier: 4.573A pdb=" N VAL D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Proline residue: D 199 - end of helix Processing helix chain 'D' and resid 215 through 220 removed outlier: 4.320A pdb=" N PHE D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.693A pdb=" N ARG D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 removed outlier: 3.788A pdb=" N TRP D 288 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 32 removed outlier: 3.812A pdb=" N GLY H 32 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 45 Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 56 through 62 removed outlier: 3.551A pdb=" N LEU H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.678A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 Processing helix chain 'H' and resid 106 through 114 Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 167 through 178 removed outlier: 4.083A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 188 removed outlier: 3.927A pdb=" N LEU H 186 " --> pdb=" O GLY H 182 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 214 removed outlier: 4.023A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN H 206 " --> pdb=" O GLN H 202 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER H 214 " --> pdb=" O MET H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 232 removed outlier: 4.012A pdb=" N THR H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 236 No H-bonds generated for 'chain 'H' and resid 234 through 236' Processing helix chain 'H' and resid 237 through 260 removed outlier: 3.546A pdb=" N ARG H 241 " --> pdb=" O GLU H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 296 removed outlier: 4.104A pdb=" N ILE H 292 " --> pdb=" O GLY H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 32 Processing helix chain 'I' and resid 34 through 45 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 62 removed outlier: 3.572A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 89 through 97 Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 167 through 178 removed outlier: 3.836A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 removed outlier: 3.720A pdb=" N VAL I 185 " --> pdb=" O SER I 181 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU I 186 " --> pdb=" O GLY I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 212 removed outlier: 4.013A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.726A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 289 through 296 Processing helix chain 'J' and resid 24 through 32 removed outlier: 3.620A pdb=" N GLY J 32 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 45 removed outlier: 3.961A pdb=" N VAL J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 67 through 81 removed outlier: 3.645A pdb=" N LYS J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 98 removed outlier: 3.502A pdb=" N SER J 97 " --> pdb=" O HIS J 93 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 113 Processing helix chain 'J' and resid 132 through 144 Processing helix chain 'J' and resid 167 through 179 removed outlier: 3.881A pdb=" N LEU J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 188 Processing helix chain 'J' and resid 196 through 212 removed outlier: 4.035A pdb=" N LEU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR J 205 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.677A pdb=" N TYR J 232 " --> pdb=" O TYR J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 237 through 260 Processing helix chain 'J' and resid 289 through 296 Processing helix chain 'K' and resid 26 through 31 removed outlier: 4.024A pdb=" N GLN K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 56 through 63 removed outlier: 3.540A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.758A pdb=" N ASP K 72 " --> pdb=" O GLU K 68 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 97 Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 132 through 145 removed outlier: 4.503A pdb=" N GLN K 145 " --> pdb=" O ALA K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 removed outlier: 4.041A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 211 Processing helix chain 'K' and resid 225 through 232 Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.955A pdb=" N ILE K 292 " --> pdb=" O GLY K 288 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA K 293 " --> pdb=" O GLY K 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 66 through 67 removed outlier: 6.637A pdb=" N GLU A 77 " --> pdb=" O CYS A 144 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU A 146 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 79 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU A 148 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 81 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 190 " --> pdb=" O CYS A 144 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 194 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP A 42 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ALA A 193 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU A 44 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR A 195 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE A 46 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 43 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N MET A 239 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU A 45 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE A 241 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N HIS A 47 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 270 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 266 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 306 through 309 removed outlier: 3.667A pdb=" N THR B 248 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS C 85 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 87 through 88 removed outlier: 5.564A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA E 217 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'F' and resid 333 through 336 removed outlier: 6.305A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU F 219 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR F 266 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL F 221 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET F 158 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP F 222 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE F 160 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AA7, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AA8, first strand: chain 'G' and resid 333 through 335 removed outlier: 3.665A pdb=" N GLY G 333 " --> pdb=" O ASN G 330 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASN G 267 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET G 125 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 262 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS G 156 " --> pdb=" O TYR G 216 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU G 218 " --> pdb=" O LYS G 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB1, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB3, first strand: chain 'C' and resid 208 through 212 removed outlier: 3.636A pdb=" N ASP C 159 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU C 154 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE C 240 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL C 156 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP C 242 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE C 158 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ARG C 237 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ILE C 281 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 239 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N THR C 283 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL C 241 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 322 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 286 through 289 Processing sheet with id=AB5, first strand: chain 'D' and resid 179 through 183 removed outlier: 5.528A pdb=" N GLY D 136 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 209 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N LEU D 254 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 210 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE D 256 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE D 212 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR D 103 " --> pdb=" O CYS D 255 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ASN D 257 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 105 " --> pdb=" O ASN D 257 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE D 102 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU D 296 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU D 104 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA D 298 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA D 106 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ARG D 300 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG D 295 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA D 312 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG D 313 " --> pdb=" O TYR D 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 259 through 261 Processing sheet with id=AB7, first strand: chain 'H' and resid 333 through 335 removed outlier: 6.279A pdb=" N ARG H 299 " --> pdb=" O TYR H 315 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR H 123 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN H 267 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET H 125 " --> pdb=" O ASN H 267 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU H 219 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR H 266 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL H 221 " --> pdb=" O THR H 266 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 269 through 271 Processing sheet with id=AB9, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AC1, first strand: chain 'I' and resid 333 through 335 removed outlier: 6.413A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE I 122 " --> pdb=" O THR I 298 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU I 300 " --> pdb=" O ILE I 122 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU I 124 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU I 302 " --> pdb=" O GLU I 124 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE I 126 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N LYS I 304 " --> pdb=" O PHE I 126 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY I 127 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS I 156 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 218 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE I 220 " --> pdb=" O MET I 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AC3, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'J' and resid 333 through 335 removed outlier: 3.567A pdb=" N CYS J 312 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG J 299 " --> pdb=" O TYR J 315 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE J 122 " --> pdb=" O THR J 298 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU J 300 " --> pdb=" O ILE J 122 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU J 124 " --> pdb=" O LEU J 300 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU J 302 " --> pdb=" O GLU J 124 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE J 126 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N LYS J 304 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR J 123 " --> pdb=" O ILE J 265 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASN J 267 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET J 125 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA J 262 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS J 156 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU J 219 " --> pdb=" O LYS J 156 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET J 158 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL J 221 " --> pdb=" O MET J 158 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE J 160 " --> pdb=" O VAL J 221 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 269 through 270 removed outlier: 3.711A pdb=" N LYS J 285 " --> pdb=" O VAL J 270 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AC7, first strand: chain 'K' and resid 189 through 193 removed outlier: 6.871A pdb=" N ALA K 157 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ALA K 192 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR K 159 " --> pdb=" O ALA K 192 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL K 270 " --> pdb=" O LYS K 285 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS K 285 " --> pdb=" O VAL K 270 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 189 through 193 removed outlier: 6.871A pdb=" N ALA K 157 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ALA K 192 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR K 159 " --> pdb=" O ALA K 192 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR K 123 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN K 267 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET K 125 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL K 269 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY K 127 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS K 312 " --> pdb=" O ALA K 325 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY K 335 " --> pdb=" O ALA K 328 " (cutoff:3.500A) 1294 hydrogen bonds defined for protein. 3657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8576 1.34 - 1.45: 4378 1.45 - 1.57: 15737 1.57 - 1.69: 234 1.69 - 1.81: 228 Bond restraints: 29153 Sorted by residual: bond pdb=" CA VAL D 198 " pdb=" CB VAL D 198 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.95e+00 bond pdb=" C3' DC M 5 " pdb=" O3' DC M 5 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" C1' DC M 31 " pdb=" N1 DC M 31 " ideal model delta sigma weight residual 1.490 1.527 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CB ARG F 130 " pdb=" CG ARG F 130 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 29148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 39588 2.46 - 4.92: 196 4.92 - 7.37: 22 7.37 - 9.83: 9 9.83 - 12.29: 13 Bond angle restraints: 39828 Sorted by residual: angle pdb=" N VAL C 151 " pdb=" CA VAL C 151 " pdb=" C VAL C 151 " ideal model delta sigma weight residual 113.53 108.27 5.26 9.80e-01 1.04e+00 2.88e+01 angle pdb=" O3' DC N 22 " pdb=" P DT N 23 " pdb=" OP2 DT N 23 " ideal model delta sigma weight residual 108.00 120.29 -12.29 3.00e+00 1.11e-01 1.68e+01 angle pdb=" OP1 DT N 23 " pdb=" P DT N 23 " pdb=" OP2 DT N 23 " ideal model delta sigma weight residual 120.00 108.54 11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" OP1 DC O 34 " pdb=" P DC O 34 " pdb=" OP2 DC O 34 " ideal model delta sigma weight residual 120.00 109.06 10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" OP1 DC O 33 " pdb=" P DC O 33 " pdb=" OP2 DC O 33 " ideal model delta sigma weight residual 120.00 109.09 10.91 3.00e+00 1.11e-01 1.32e+01 ... (remaining 39823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 16884 35.00 - 70.01: 669 70.01 - 105.01: 36 105.01 - 140.01: 0 140.01 - 175.01: 2 Dihedral angle restraints: 17591 sinusoidal: 7824 harmonic: 9767 Sorted by residual: dihedral pdb=" CA GLU E 128 " pdb=" C GLU E 128 " pdb=" N PHE E 129 " pdb=" CA PHE E 129 " ideal model delta harmonic sigma weight residual 180.00 154.20 25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" C4' DC O 34 " pdb=" C3' DC O 34 " pdb=" O3' DC O 34 " pdb=" P DC O 35 " ideal model delta sinusoidal sigma weight residual -140.00 35.01 -175.01 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC M 5 " pdb=" C3' DC M 5 " pdb=" O3' DC M 5 " pdb=" P DC M 6 " ideal model delta sinusoidal sigma weight residual 220.00 65.19 154.81 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 17588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4351 0.092 - 0.183: 219 0.183 - 0.275: 0 0.275 - 0.367: 2 0.367 - 0.458: 9 Chirality restraints: 4581 Sorted by residual: chirality pdb=" P DT N 23 " pdb=" OP1 DT N 23 " pdb=" OP2 DT N 23 " pdb=" O5' DT N 23 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" P DC O 34 " pdb=" OP1 DC O 34 " pdb=" OP2 DC O 34 " pdb=" O5' DC O 34 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" P DC M 11 " pdb=" OP1 DC M 11 " pdb=" OP2 DC M 11 " pdb=" O5' DC M 11 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 4578 not shown) Planarity restraints: 4779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 129 " 0.011 2.00e-02 2.50e+03 1.40e-02 3.44e+00 pdb=" CG PHE E 129 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE E 129 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE E 129 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 129 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 129 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 129 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 224 " 0.008 2.00e-02 2.50e+03 1.22e-02 2.97e+00 pdb=" CG TYR C 224 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 224 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C 224 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 224 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 224 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 224 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 224 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 342 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO C 343 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 343 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 343 " -0.021 5.00e-02 4.00e+02 ... (remaining 4776 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 256 2.58 - 3.16: 22180 3.16 - 3.74: 43785 3.74 - 4.32: 59503 4.32 - 4.90: 101005 Nonbonded interactions: 226729 Sorted by model distance: nonbonded pdb=" O2B ATP E 401 " pdb="MG MG E 402 " model vdw 2.000 2.170 nonbonded pdb=" OG1 THR J 134 " pdb="MG MG J 403 " model vdw 2.023 2.170 nonbonded pdb=" O2B ATP I 401 " pdb="MG MG I 402 " model vdw 2.043 2.170 nonbonded pdb=" O2A ATP D 401 " pdb="MG MG D 402 " model vdw 2.046 2.170 nonbonded pdb=" O3B ATP D 401 " pdb="MG MG D 402 " model vdw 2.051 2.170 ... (remaining 226724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'F' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'G' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'H' and (resid 21 through 273 or resid 283 through 339)) selection = (chain 'I' and resid 21 through 339) selection = (chain 'J' and resid 21 through 339) selection = (chain 'K' and resid 21 through 339) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 30.140 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29153 Z= 0.103 Angle : 0.526 12.289 39828 Z= 0.266 Chirality : 0.043 0.458 4581 Planarity : 0.003 0.038 4779 Dihedral : 17.025 175.013 11311 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3379 helix: 1.13 (0.14), residues: 1431 sheet: 0.71 (0.23), residues: 610 loop : -1.03 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 130 TYR 0.029 0.001 TYR C 224 PHE 0.032 0.001 PHE E 129 TRP 0.014 0.001 TRP A 231 HIS 0.004 0.000 HIS K 138 Details of bonding type rmsd covalent geometry : bond 0.00210 (29153) covalent geometry : angle 0.52608 (39828) hydrogen bonds : bond 0.17990 ( 1357) hydrogen bonds : angle 6.44663 ( 3801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6348 (tmm) cc_final: 0.5066 (ppp) REVERT: B 174 ASP cc_start: 0.8122 (m-30) cc_final: 0.7913 (m-30) REVERT: B 249 ASN cc_start: 0.8674 (t0) cc_final: 0.8363 (t0) REVERT: B 253 ARG cc_start: 0.6070 (mmp-170) cc_final: 0.5762 (mmm160) REVERT: F 34 ASN cc_start: 0.8344 (t0) cc_final: 0.8060 (t0) REVERT: G 285 LYS cc_start: 0.8872 (ptpt) cc_final: 0.8521 (ptmm) REVERT: A 268 HIS cc_start: 0.6284 (m-70) cc_final: 0.6039 (m90) REVERT: C 167 ASP cc_start: 0.8031 (m-30) cc_final: 0.7392 (t0) REVERT: D 72 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8705 (mmpt) REVERT: H 31 CYS cc_start: 0.8279 (m) cc_final: 0.8034 (m) REVERT: H 34 ASN cc_start: 0.7928 (t0) cc_final: 0.7694 (t0) REVERT: H 326 MET cc_start: 0.8905 (ttm) cc_final: 0.8660 (ttp) REVERT: I 247 ARG cc_start: 0.8995 (mmt180) cc_final: 0.8710 (tpp80) REVERT: J 332 ASP cc_start: 0.8442 (p0) cc_final: 0.8151 (p0) REVERT: K 267 ASN cc_start: 0.7650 (t0) cc_final: 0.7281 (t0) outliers start: 0 outliers final: 1 residues processed: 359 average time/residue: 0.8518 time to fit residues: 345.7576 Evaluate side-chains 231 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN G 202 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN D 80 GLN D 148 HIS D 322 HIS J 23 GLN J 36 ASN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.118428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076305 restraints weight = 52992.692| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.65 r_work: 0.2802 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 29153 Z= 0.336 Angle : 0.660 9.762 39828 Z= 0.350 Chirality : 0.045 0.181 4581 Planarity : 0.005 0.072 4779 Dihedral : 16.729 172.371 5045 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.54 % Allowed : 11.96 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3379 helix: 0.98 (0.14), residues: 1487 sheet: 0.70 (0.22), residues: 585 loop : -1.25 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 306 TYR 0.023 0.002 TYR C 224 PHE 0.027 0.002 PHE K 129 TRP 0.006 0.001 TRP A 231 HIS 0.007 0.001 HIS I 244 Details of bonding type rmsd covalent geometry : bond 0.00793 (29153) covalent geometry : angle 0.65992 (39828) hydrogen bonds : bond 0.05755 ( 1357) hydrogen bonds : angle 5.11313 ( 3801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6037 (tmm) cc_final: 0.4807 (ppp) REVERT: B 174 ASP cc_start: 0.8313 (m-30) cc_final: 0.7999 (m-30) REVERT: B 186 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8849 (ttp80) REVERT: B 249 ASN cc_start: 0.8753 (t0) cc_final: 0.8478 (t0) REVERT: B 253 ARG cc_start: 0.6245 (mmp-170) cc_final: 0.5842 (mmm160) REVERT: B 292 MET cc_start: 0.6837 (mmp) cc_final: 0.6416 (mmm) REVERT: F 34 ASN cc_start: 0.7967 (t0) cc_final: 0.7626 (t0) REVERT: G 64 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8446 (mttt) REVERT: A 136 MET cc_start: 0.8555 (tmm) cc_final: 0.8006 (pp-130) REVERT: A 143 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8649 (mp) REVERT: A 179 CYS cc_start: 0.8547 (t) cc_final: 0.8329 (t) REVERT: A 268 HIS cc_start: 0.6496 (m-70) cc_final: 0.6290 (m-70) REVERT: C 33 GLN cc_start: 0.6261 (mm-40) cc_final: 0.6030 (mm110) REVERT: C 85 CYS cc_start: 0.7936 (m) cc_final: 0.7578 (m) REVERT: C 167 ASP cc_start: 0.8090 (m-30) cc_final: 0.7449 (t0) REVERT: D 295 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8503 (mtm180) REVERT: H 31 CYS cc_start: 0.8207 (m) cc_final: 0.7946 (m) REVERT: H 34 ASN cc_start: 0.7520 (t0) cc_final: 0.7301 (t0) REVERT: J 332 ASP cc_start: 0.8461 (p0) cc_final: 0.8258 (p0) REVERT: K 50 GLU cc_start: 0.7802 (pp20) cc_final: 0.7512 (pp20) outliers start: 43 outliers final: 11 residues processed: 263 average time/residue: 0.7229 time to fit residues: 220.5472 Evaluate side-chains 229 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain K residue 60 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 82 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 342 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 HIS C 294 GLN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.080056 restraints weight = 53294.776| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.62 r_work: 0.2876 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29153 Z= 0.120 Angle : 0.520 10.315 39828 Z= 0.274 Chirality : 0.040 0.168 4581 Planarity : 0.003 0.043 4779 Dihedral : 16.463 174.741 5043 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.22 % Allowed : 14.46 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3379 helix: 1.18 (0.14), residues: 1496 sheet: 0.79 (0.22), residues: 572 loop : -1.22 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 306 TYR 0.026 0.001 TYR C 224 PHE 0.017 0.001 PHE B 270 TRP 0.004 0.001 TRP A 231 HIS 0.003 0.001 HIS H 138 Details of bonding type rmsd covalent geometry : bond 0.00269 (29153) covalent geometry : angle 0.51952 (39828) hydrogen bonds : bond 0.03567 ( 1357) hydrogen bonds : angle 4.46384 ( 3801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6190 (tmm) cc_final: 0.4839 (ppp) REVERT: B 253 ARG cc_start: 0.6171 (mmp-170) cc_final: 0.5764 (mmm160) REVERT: B 292 MET cc_start: 0.6848 (mmp) cc_final: 0.6472 (mmm) REVERT: G 285 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8527 (ptmm) REVERT: A 82 ASP cc_start: 0.8002 (t0) cc_final: 0.7692 (t0) REVERT: A 179 CYS cc_start: 0.8241 (t) cc_final: 0.8017 (t) REVERT: A 223 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7426 (p90) REVERT: A 268 HIS cc_start: 0.6559 (m-70) cc_final: 0.5753 (m90) REVERT: C 33 GLN cc_start: 0.6320 (mm-40) cc_final: 0.6029 (mm-40) REVERT: C 45 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: C 85 CYS cc_start: 0.7843 (m) cc_final: 0.7474 (m) REVERT: C 167 ASP cc_start: 0.7901 (m-30) cc_final: 0.7256 (t0) REVERT: C 327 TYR cc_start: 0.8690 (t80) cc_final: 0.8436 (t80) REVERT: H 31 CYS cc_start: 0.8185 (m) cc_final: 0.7878 (m) REVERT: H 247 ARG cc_start: 0.8712 (ttp-110) cc_final: 0.8466 (ttm110) REVERT: J 332 ASP cc_start: 0.8440 (p0) cc_final: 0.8220 (p0) outliers start: 34 outliers final: 8 residues processed: 276 average time/residue: 0.6539 time to fit residues: 210.7518 Evaluate side-chains 235 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 224 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 149 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 177 optimal weight: 1.9990 chunk 311 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN C 187 HIS ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.119854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.077890 restraints weight = 52552.839| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.37 r_work: 0.2850 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29153 Z= 0.201 Angle : 0.560 11.888 39828 Z= 0.295 Chirality : 0.041 0.152 4581 Planarity : 0.004 0.044 4779 Dihedral : 16.583 173.481 5043 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.04 % Allowed : 16.40 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3379 helix: 1.22 (0.14), residues: 1483 sheet: 0.72 (0.22), residues: 595 loop : -1.21 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 306 TYR 0.025 0.001 TYR C 224 PHE 0.025 0.002 PHE K 129 TRP 0.007 0.001 TRP A 231 HIS 0.004 0.001 HIS I 244 Details of bonding type rmsd covalent geometry : bond 0.00474 (29153) covalent geometry : angle 0.55995 (39828) hydrogen bonds : bond 0.04371 ( 1357) hydrogen bonds : angle 4.52645 ( 3801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6198 (tmm) cc_final: 0.4895 (ppp) REVERT: B 174 ASP cc_start: 0.8301 (m-30) cc_final: 0.8090 (m-30) REVERT: B 186 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8837 (ttp80) REVERT: B 249 ASN cc_start: 0.8823 (t0) cc_final: 0.8522 (t0) REVERT: B 292 MET cc_start: 0.6935 (mmp) cc_final: 0.6534 (mmm) REVERT: G 27 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8328 (mtp180) REVERT: G 64 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8457 (mttt) REVERT: A 82 ASP cc_start: 0.8065 (t0) cc_final: 0.7653 (t0) REVERT: A 148 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8283 (pt) REVERT: A 149 ASP cc_start: 0.7771 (t0) cc_final: 0.7500 (t0) REVERT: A 223 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7457 (p90) REVERT: A 268 HIS cc_start: 0.6642 (m-70) cc_final: 0.5852 (m90) REVERT: C 33 GLN cc_start: 0.6605 (mm-40) cc_final: 0.6296 (mm-40) REVERT: C 85 CYS cc_start: 0.7912 (m) cc_final: 0.7526 (m) REVERT: C 167 ASP cc_start: 0.8154 (m-30) cc_final: 0.7400 (t0) REVERT: D 295 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8527 (mtm180) REVERT: H 31 CYS cc_start: 0.8269 (m) cc_final: 0.7943 (m) REVERT: H 247 ARG cc_start: 0.8974 (ttp-110) cc_final: 0.8738 (ttm110) REVERT: H 306 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7658 (mmt-90) REVERT: I 110 ASP cc_start: 0.8630 (m-30) cc_final: 0.8403 (m-30) REVERT: J 332 ASP cc_start: 0.8557 (p0) cc_final: 0.8324 (p0) REVERT: K 62 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8396 (t0) REVERT: K 140 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9118 (mm) outliers start: 57 outliers final: 21 residues processed: 266 average time/residue: 0.6979 time to fit residues: 216.2645 Evaluate side-chains 246 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 261 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 316 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 232 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 101 optimal weight: 0.0170 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 HIS D 9 ASN I 36 ASN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079468 restraints weight = 52431.052| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.45 r_work: 0.2871 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29153 Z= 0.141 Angle : 0.528 10.671 39828 Z= 0.277 Chirality : 0.040 0.215 4581 Planarity : 0.003 0.047 4779 Dihedral : 16.469 174.178 5043 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.72 % Allowed : 17.47 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3379 helix: 1.29 (0.14), residues: 1484 sheet: 0.76 (0.22), residues: 595 loop : -1.19 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 306 TYR 0.028 0.001 TYR C 224 PHE 0.019 0.001 PHE B 270 TRP 0.005 0.001 TRP A 231 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00327 (29153) covalent geometry : angle 0.52815 (39828) hydrogen bonds : bond 0.03603 ( 1357) hydrogen bonds : angle 4.31428 ( 3801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6158 (tmm) cc_final: 0.4950 (ppp) REVERT: B 186 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8769 (ttp80) REVERT: B 228 MET cc_start: 0.9562 (mmp) cc_final: 0.9295 (mmp) REVERT: B 249 ASN cc_start: 0.8638 (t0) cc_final: 0.8327 (t0) REVERT: B 292 MET cc_start: 0.6866 (mmp) cc_final: 0.6484 (mmm) REVERT: F 39 LYS cc_start: 0.8921 (tppp) cc_final: 0.8685 (tppp) REVERT: G 27 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8142 (mtp180) REVERT: G 64 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8383 (mttt) REVERT: G 285 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8395 (ptpp) REVERT: A 82 ASP cc_start: 0.7936 (t0) cc_final: 0.7565 (t0) REVERT: A 148 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8297 (pt) REVERT: A 149 ASP cc_start: 0.7731 (t0) cc_final: 0.7433 (t0) REVERT: A 185 ASN cc_start: 0.8199 (m-40) cc_final: 0.7447 (p0) REVERT: A 223 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7449 (p90) REVERT: A 268 HIS cc_start: 0.6579 (m-70) cc_final: 0.5769 (m90) REVERT: C 33 GLN cc_start: 0.6508 (mm-40) cc_final: 0.6135 (mm-40) REVERT: C 45 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: C 85 CYS cc_start: 0.7812 (m) cc_final: 0.7437 (m) REVERT: C 167 ASP cc_start: 0.7959 (m-30) cc_final: 0.7267 (t0) REVERT: H 31 CYS cc_start: 0.8129 (m) cc_final: 0.7817 (m) REVERT: H 306 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7217 (mmt180) REVERT: K 62 ASN cc_start: 0.8489 (t0) cc_final: 0.8286 (t0) REVERT: K 140 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9152 (mm) outliers start: 48 outliers final: 16 residues processed: 268 average time/residue: 0.7608 time to fit residues: 236.0374 Evaluate side-chains 248 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain K residue 140 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 246 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 133 optimal weight: 0.0270 chunk 261 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 253 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 HIS D 9 ASN I 36 ASN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.121060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.077407 restraints weight = 53104.649| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.68 r_work: 0.2861 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29153 Z= 0.149 Angle : 0.531 11.270 39828 Z= 0.277 Chirality : 0.040 0.231 4581 Planarity : 0.003 0.045 4779 Dihedral : 16.445 174.197 5043 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.90 % Allowed : 18.15 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3379 helix: 1.31 (0.14), residues: 1485 sheet: 0.75 (0.22), residues: 595 loop : -1.16 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 27 TYR 0.028 0.001 TYR C 224 PHE 0.020 0.001 PHE B 270 TRP 0.006 0.001 TRP A 231 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00348 (29153) covalent geometry : angle 0.53115 (39828) hydrogen bonds : bond 0.03636 ( 1357) hydrogen bonds : angle 4.28221 ( 3801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6204 (tmm) cc_final: 0.5038 (ppp) REVERT: B 186 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8782 (ttp80) REVERT: B 228 MET cc_start: 0.9575 (mmp) cc_final: 0.9311 (mmp) REVERT: B 249 ASN cc_start: 0.8662 (t0) cc_final: 0.8322 (t0) REVERT: B 292 MET cc_start: 0.6853 (mmp) cc_final: 0.6439 (mmm) REVERT: F 39 LYS cc_start: 0.8919 (tppp) cc_final: 0.8678 (tppp) REVERT: G 27 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8154 (mtp180) REVERT: G 64 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8398 (mttt) REVERT: G 285 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8392 (ptpp) REVERT: E 96 ARG cc_start: 0.6053 (OUTLIER) cc_final: 0.5186 (mmm160) REVERT: A 82 ASP cc_start: 0.7922 (t0) cc_final: 0.7468 (t0) REVERT: A 148 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8281 (pt) REVERT: A 149 ASP cc_start: 0.7736 (t0) cc_final: 0.7419 (t0) REVERT: A 179 CYS cc_start: 0.8016 (t) cc_final: 0.7746 (t) REVERT: A 185 ASN cc_start: 0.8119 (m-40) cc_final: 0.7402 (p0) REVERT: A 223 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7452 (p90) REVERT: A 268 HIS cc_start: 0.6536 (m-70) cc_final: 0.5753 (m90) REVERT: C 33 GLN cc_start: 0.6317 (mm-40) cc_final: 0.5931 (mm-40) REVERT: C 45 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: C 85 CYS cc_start: 0.7814 (m) cc_final: 0.7427 (m) REVERT: C 167 ASP cc_start: 0.7992 (m-30) cc_final: 0.7263 (t0) REVERT: H 31 CYS cc_start: 0.8092 (m) cc_final: 0.7778 (m) REVERT: H 306 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7217 (mmt180) REVERT: J 332 ASP cc_start: 0.8481 (p0) cc_final: 0.8237 (p0) REVERT: K 140 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9152 (mm) REVERT: K 158 MET cc_start: 0.7440 (ttm) cc_final: 0.6784 (mtp) outliers start: 53 outliers final: 22 residues processed: 271 average time/residue: 0.7193 time to fit residues: 227.1151 Evaluate side-chains 252 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 261 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 0.3980 chunk 330 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 338 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 336 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 203 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 93 GLN C 97 GLN C 187 HIS D 9 ASN H 330 ASN I 36 ASN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.120620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.079242 restraints weight = 52388.301| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.50 r_work: 0.2857 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29153 Z= 0.166 Angle : 0.554 11.667 39828 Z= 0.287 Chirality : 0.040 0.240 4581 Planarity : 0.004 0.052 4779 Dihedral : 16.469 173.986 5043 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.22 % Allowed : 18.55 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3379 helix: 1.29 (0.14), residues: 1485 sheet: 0.72 (0.22), residues: 594 loop : -1.15 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 247 TYR 0.030 0.001 TYR C 224 PHE 0.020 0.001 PHE B 270 TRP 0.006 0.001 TRP A 231 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00388 (29153) covalent geometry : angle 0.55420 (39828) hydrogen bonds : bond 0.03799 ( 1357) hydrogen bonds : angle 4.31417 ( 3801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6201 (tmm) cc_final: 0.4898 (ppp) REVERT: B 186 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8792 (ttp80) REVERT: B 224 LEU cc_start: 0.9245 (mt) cc_final: 0.8755 (tm) REVERT: B 228 MET cc_start: 0.9555 (mmp) cc_final: 0.9126 (mmp) REVERT: B 249 ASN cc_start: 0.8742 (t0) cc_final: 0.8394 (t0) REVERT: B 292 MET cc_start: 0.6876 (mmp) cc_final: 0.6589 (mmp) REVERT: F 39 LYS cc_start: 0.8920 (tppp) cc_final: 0.8681 (tppp) REVERT: G 27 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8117 (mtp180) REVERT: G 64 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8403 (mttt) REVERT: G 285 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8397 (ptpp) REVERT: E 96 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.5212 (mmm160) REVERT: A 82 ASP cc_start: 0.7935 (t0) cc_final: 0.7514 (t0) REVERT: A 148 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8258 (pt) REVERT: A 149 ASP cc_start: 0.7801 (t0) cc_final: 0.7471 (OUTLIER) REVERT: A 185 ASN cc_start: 0.8095 (m-40) cc_final: 0.7387 (p0) REVERT: A 223 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7411 (p90) REVERT: A 246 ASP cc_start: 0.4382 (m-30) cc_final: 0.3900 (t70) REVERT: A 268 HIS cc_start: 0.6553 (m-70) cc_final: 0.5766 (m90) REVERT: C 33 GLN cc_start: 0.6273 (mm-40) cc_final: 0.5932 (mm-40) REVERT: C 45 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: C 85 CYS cc_start: 0.7813 (m) cc_final: 0.7440 (m) REVERT: C 167 ASP cc_start: 0.8011 (m-30) cc_final: 0.7277 (t0) REVERT: H 31 CYS cc_start: 0.8102 (m) cc_final: 0.7784 (m) REVERT: H 64 LYS cc_start: 0.7867 (pptt) cc_final: 0.7567 (mmtp) REVERT: H 306 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7221 (mmt180) REVERT: I 30 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: J 332 ASP cc_start: 0.8530 (p0) cc_final: 0.8304 (p0) REVERT: K 140 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9146 (mm) outliers start: 62 outliers final: 26 residues processed: 269 average time/residue: 0.6874 time to fit residues: 217.2761 Evaluate side-chains 258 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 261 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 213 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 340 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 295 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 325 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 253 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN G 244 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN H 330 ASN I 36 ASN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081654 restraints weight = 52454.416| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.60 r_work: 0.2911 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29153 Z= 0.109 Angle : 0.534 12.669 39828 Z= 0.272 Chirality : 0.039 0.244 4581 Planarity : 0.003 0.051 4779 Dihedral : 16.289 175.159 5043 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.50 % Allowed : 19.69 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.15), residues: 3379 helix: 1.33 (0.14), residues: 1493 sheet: 0.85 (0.22), residues: 574 loop : -1.11 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 27 TYR 0.030 0.001 TYR C 224 PHE 0.031 0.001 PHE E 279 TRP 0.005 0.001 TRP D 47 HIS 0.003 0.000 HIS H 138 Details of bonding type rmsd covalent geometry : bond 0.00242 (29153) covalent geometry : angle 0.53378 (39828) hydrogen bonds : bond 0.02873 ( 1357) hydrogen bonds : angle 4.09975 ( 3801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6123 (tmm) cc_final: 0.4963 (ppp) REVERT: B 3 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7534 (p) REVERT: B 15 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7945 (pp20) REVERT: B 224 LEU cc_start: 0.9152 (mt) cc_final: 0.8690 (tm) REVERT: B 228 MET cc_start: 0.9548 (mmp) cc_final: 0.9088 (mmp) REVERT: B 243 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7332 (mmt) REVERT: B 249 ASN cc_start: 0.8532 (t0) cc_final: 0.8238 (t0) REVERT: B 253 ARG cc_start: 0.5979 (mmm160) cc_final: 0.5610 (mmm160) REVERT: B 292 MET cc_start: 0.6848 (mmp) cc_final: 0.6609 (mmp) REVERT: F 39 LYS cc_start: 0.8912 (tppp) cc_final: 0.8663 (tppp) REVERT: G 27 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8112 (mtp180) REVERT: G 285 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8613 (ptmm) REVERT: A 59 TYR cc_start: 0.8426 (m-10) cc_final: 0.8066 (m-10) REVERT: A 82 ASP cc_start: 0.7814 (t0) cc_final: 0.7351 (t0) REVERT: A 148 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8232 (pt) REVERT: A 149 ASP cc_start: 0.7778 (t0) cc_final: 0.7461 (t0) REVERT: A 185 ASN cc_start: 0.8098 (m-40) cc_final: 0.7394 (p0) REVERT: A 223 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7455 (p90) REVERT: A 246 ASP cc_start: 0.4070 (m-30) cc_final: 0.3579 (t70) REVERT: A 268 HIS cc_start: 0.6517 (m-70) cc_final: 0.5766 (m90) REVERT: C 33 GLN cc_start: 0.6422 (mm-40) cc_final: 0.6087 (mm-40) REVERT: C 45 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: C 85 CYS cc_start: 0.7776 (m) cc_final: 0.7404 (m) REVERT: C 167 ASP cc_start: 0.7909 (m-30) cc_final: 0.7160 (t0) REVERT: C 327 TYR cc_start: 0.8631 (t80) cc_final: 0.8430 (t80) REVERT: H 31 CYS cc_start: 0.8059 (m) cc_final: 0.7733 (m) REVERT: H 247 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8202 (mtm110) REVERT: H 306 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7202 (mmt180) REVERT: I 30 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: J 332 ASP cc_start: 0.8471 (p0) cc_final: 0.8204 (p0) REVERT: K 140 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9171 (mm) REVERT: K 158 MET cc_start: 0.7281 (ttm) cc_final: 0.6631 (mtp) outliers start: 42 outliers final: 14 residues processed: 279 average time/residue: 0.6043 time to fit residues: 197.9382 Evaluate side-chains 256 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain K residue 140 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 318 optimal weight: 0.0870 chunk 207 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 325 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 337 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 HIS C 294 GLN H 330 ASN I 36 ASN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.119379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.076995 restraints weight = 52591.078| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.65 r_work: 0.2834 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 29153 Z= 0.241 Angle : 0.613 12.950 39828 Z= 0.318 Chirality : 0.043 0.257 4581 Planarity : 0.004 0.051 4779 Dihedral : 16.567 172.871 5043 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.40 % Allowed : 20.48 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3379 helix: 1.27 (0.14), residues: 1485 sheet: 0.61 (0.22), residues: 603 loop : -1.14 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 247 TYR 0.031 0.002 TYR C 224 PHE 0.025 0.002 PHE E 279 TRP 0.007 0.001 TRP A 231 HIS 0.005 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00572 (29153) covalent geometry : angle 0.61308 (39828) hydrogen bonds : bond 0.04556 ( 1357) hydrogen bonds : angle 4.45770 ( 3801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6168 (tmm) cc_final: 0.4846 (ppp) REVERT: B 224 LEU cc_start: 0.9312 (mt) cc_final: 0.8962 (tm) REVERT: B 228 MET cc_start: 0.9606 (mmp) cc_final: 0.9387 (mmp) REVERT: B 249 ASN cc_start: 0.8921 (t0) cc_final: 0.8610 (t0) REVERT: B 292 MET cc_start: 0.6988 (mmp) cc_final: 0.6597 (mmp) REVERT: F 39 LYS cc_start: 0.8934 (tppp) cc_final: 0.8685 (tppp) REVERT: G 27 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8328 (mtp180) REVERT: G 64 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8448 (mttt) REVERT: A 131 TYR cc_start: 0.7660 (m-10) cc_final: 0.7404 (m-10) REVERT: A 148 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8219 (pt) REVERT: A 149 ASP cc_start: 0.7852 (t0) cc_final: 0.7357 (t0) REVERT: A 185 ASN cc_start: 0.8117 (m-40) cc_final: 0.7344 (p0) REVERT: A 223 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7495 (p90) REVERT: A 268 HIS cc_start: 0.6643 (m-70) cc_final: 0.5812 (m90) REVERT: C 33 GLN cc_start: 0.6187 (mm-40) cc_final: 0.5869 (mm-40) REVERT: C 45 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: C 85 CYS cc_start: 0.7982 (m) cc_final: 0.7571 (m) REVERT: C 167 ASP cc_start: 0.8255 (m-30) cc_final: 0.7410 (t0) REVERT: H 31 CYS cc_start: 0.8244 (m) cc_final: 0.7878 (m) REVERT: H 247 ARG cc_start: 0.8955 (ttm-80) cc_final: 0.8564 (mtp180) REVERT: H 306 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7499 (mmt180) REVERT: K 140 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9159 (mm) outliers start: 39 outliers final: 17 residues processed: 242 average time/residue: 0.6422 time to fit residues: 183.1248 Evaluate side-chains 239 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain K residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 193 optimal weight: 0.6980 chunk 235 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 250 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 chunk 313 optimal weight: 9.9990 chunk 220 optimal weight: 0.0980 chunk 32 optimal weight: 9.9990 chunk 334 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 HIS I 36 ASN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.122315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.080633 restraints weight = 52324.945| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.57 r_work: 0.2889 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29153 Z= 0.117 Angle : 0.554 13.751 39828 Z= 0.283 Chirality : 0.040 0.264 4581 Planarity : 0.003 0.047 4779 Dihedral : 16.369 174.712 5043 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.90 % Allowed : 21.20 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.15), residues: 3379 helix: 1.35 (0.14), residues: 1490 sheet: 0.79 (0.22), residues: 574 loop : -1.10 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 27 TYR 0.032 0.001 TYR C 224 PHE 0.021 0.001 PHE B 270 TRP 0.004 0.000 TRP D 47 HIS 0.003 0.000 HIS H 138 Details of bonding type rmsd covalent geometry : bond 0.00265 (29153) covalent geometry : angle 0.55387 (39828) hydrogen bonds : bond 0.03126 ( 1357) hydrogen bonds : angle 4.16947 ( 3801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6758 Ramachandran restraints generated. 3379 Oldfield, 0 Emsley, 3379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 1.214 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: B 1 MET cc_start: 0.6115 (tmm) cc_final: 0.4819 (ppp) REVERT: B 224 LEU cc_start: 0.9189 (mt) cc_final: 0.8803 (tm) REVERT: B 228 MET cc_start: 0.9553 (mmp) cc_final: 0.9084 (mmp) REVERT: B 243 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7357 (mmt) REVERT: B 249 ASN cc_start: 0.8625 (t0) cc_final: 0.8306 (t0) REVERT: B 253 ARG cc_start: 0.5981 (mmm160) cc_final: 0.5581 (mmm160) REVERT: B 292 MET cc_start: 0.6922 (mmp) cc_final: 0.6683 (mmp) REVERT: F 39 LYS cc_start: 0.8893 (tppp) cc_final: 0.8657 (tppp) REVERT: G 27 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8135 (mtp180) REVERT: G 64 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8375 (mttt) REVERT: A 42 ASP cc_start: 0.6099 (p0) cc_final: 0.5490 (p0) REVERT: A 82 ASP cc_start: 0.7962 (t0) cc_final: 0.7621 (t0) REVERT: A 148 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8276 (pt) REVERT: A 149 ASP cc_start: 0.7823 (t0) cc_final: 0.7545 (t0) REVERT: A 185 ASN cc_start: 0.8054 (m-40) cc_final: 0.7347 (p0) REVERT: A 223 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7416 (p90) REVERT: A 246 ASP cc_start: 0.4116 (m-30) cc_final: 0.3608 (t70) REVERT: A 268 HIS cc_start: 0.6559 (m-70) cc_final: 0.5796 (m90) REVERT: C 33 GLN cc_start: 0.6295 (mm-40) cc_final: 0.5929 (mm-40) REVERT: C 45 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7390 (pm20) REVERT: C 85 CYS cc_start: 0.7824 (m) cc_final: 0.7438 (m) REVERT: C 142 VAL cc_start: 0.9021 (p) cc_final: 0.8759 (p) REVERT: C 167 ASP cc_start: 0.7941 (m-30) cc_final: 0.7203 (t0) REVERT: H 31 CYS cc_start: 0.8017 (m) cc_final: 0.7708 (m) REVERT: H 247 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8214 (mtm110) REVERT: H 306 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7220 (mmt180) REVERT: I 30 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: J 332 ASP cc_start: 0.8507 (p0) cc_final: 0.8271 (p0) REVERT: K 140 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9169 (mm) outliers start: 25 outliers final: 14 residues processed: 246 average time/residue: 0.6558 time to fit residues: 188.6906 Evaluate side-chains 249 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain K residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 328 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 81 optimal weight: 0.0670 chunk 157 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 315 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 342 optimal weight: 4.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 HIS I 36 ASN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.080902 restraints weight = 52657.661| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.71 r_work: 0.2900 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29153 Z= 0.114 Angle : 0.544 13.560 39828 Z= 0.279 Chirality : 0.039 0.260 4581 Planarity : 0.003 0.040 4779 Dihedral : 16.276 174.897 5043 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.00 % Allowed : 20.98 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 3379 helix: 1.40 (0.14), residues: 1494 sheet: 0.85 (0.22), residues: 575 loop : -1.06 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 247 TYR 0.032 0.001 TYR C 224 PHE 0.023 0.001 PHE E 279 TRP 0.002 0.000 TRP A 231 HIS 0.003 0.000 HIS H 138 Details of bonding type rmsd covalent geometry : bond 0.00256 (29153) covalent geometry : angle 0.54410 (39828) hydrogen bonds : bond 0.03030 ( 1357) hydrogen bonds : angle 4.10708 ( 3801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9015.59 seconds wall clock time: 154 minutes 27.71 seconds (9267.71 seconds total)