Starting phenix.real_space_refine on Fri May 10 08:56:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/05_2024/8wui_37855_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/05_2024/8wui_37855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/05_2024/8wui_37855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/05_2024/8wui_37855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/05_2024/8wui_37855_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wui_37855/05_2024/8wui_37855_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 92 5.16 5 C 10130 2.51 5 N 2498 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 369": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 15340 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3706 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 13, 'TRANS': 435} Chain breaks: 1 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3832 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 1 Chain: "D" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3706 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 13, 'TRANS': 435} Chain breaks: 1 Chain: "C" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3832 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 8.35, per 1000 atoms: 0.54 Number of scatterers: 15340 At special positions: 0 Unit cell: (117.52, 115.44, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 2 15.00 O 2618 8.00 N 2498 7.00 C 10130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.78 Conformation dependent library (CDL) restraints added in 2.8 seconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 10 sheets defined 59.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 115 through 133 removed outlier: 3.582A pdb=" N PHE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 182 through 207 removed outlier: 3.831A pdb=" N PHE B 201 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 202 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 242 removed outlier: 3.670A pdb=" N ILE B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 300 through 329 removed outlier: 3.508A pdb=" N ALA B 317 " --> pdb=" O MET B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.553A pdb=" N ARG B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 368 Processing helix chain 'B' and resid 383 through 399 removed outlier: 5.277A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 395 " --> pdb=" O GLN B 391 " (cutoff:3.500A) Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 499 through 508 Processing helix chain 'B' and resid 510 through 523 Processing helix chain 'A' and resid 80 through 97 removed outlier: 3.720A pdb=" N SER A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 114 through 132 Processing helix chain 'A' and resid 149 through 159 removed outlier: 4.131A pdb=" N ALA A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 removed outlier: 3.603A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 182 through 207 removed outlier: 3.767A pdb=" N TYR A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 241 removed outlier: 3.847A pdb=" N CYS A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.591A pdb=" N SER A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 329 Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 354 through 379 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 395 through 400 removed outlier: 4.102A pdb=" N LYS A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 418 removed outlier: 3.768A pdb=" N ILE A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 418 " --> pdb=" O GLN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.561A pdb=" N ILE A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.516A pdb=" N ARG A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 544 removed outlier: 4.208A pdb=" N PHE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 541 " --> pdb=" O ILE A 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 97 Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 115 through 133 removed outlier: 3.582A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 158 Processing helix chain 'D' and resid 162 through 166 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 182 through 207 removed outlier: 3.831A pdb=" N PHE D 201 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 202 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 222 removed outlier: 3.670A pdb=" N ILE D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 242 removed outlier: 4.217A pdb=" N THR D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 271 through 286 Processing helix chain 'D' and resid 300 through 329 removed outlier: 3.508A pdb=" N ALA D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 350 removed outlier: 3.553A pdb=" N ARG D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 368 Processing helix chain 'D' and resid 383 through 399 removed outlier: 5.277A pdb=" N LYS D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 395 " --> pdb=" O GLN D 391 " (cutoff:3.500A) Proline residue: D 396 - end of helix Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 473 through 478 Processing helix chain 'D' and resid 499 through 508 Processing helix chain 'D' and resid 510 through 523 Processing helix chain 'C' and resid 80 through 97 removed outlier: 3.719A pdb=" N SER C 96 " --> pdb=" O TRP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 114 through 132 Processing helix chain 'C' and resid 149 through 159 removed outlier: 4.131A pdb=" N ALA C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 167 removed outlier: 3.603A pdb=" N LEU C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 182 through 207 removed outlier: 3.767A pdb=" N TYR C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG C 197 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 241 removed outlier: 3.961A pdb=" N CYS C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 238 " --> pdb=" O CYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 271 through 286 removed outlier: 3.591A pdb=" N SER C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 329 Processing helix chain 'C' and resid 332 through 350 Processing helix chain 'C' and resid 354 through 379 Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 395 through 400 removed outlier: 4.102A pdb=" N LYS C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 418 removed outlier: 3.768A pdb=" N ILE C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG C 418 " --> pdb=" O GLN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 477 No H-bonds generated for 'chain 'C' and resid 474 through 477' Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.561A pdb=" N ILE C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 520 removed outlier: 3.516A pdb=" N ARG C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 544 removed outlier: 4.208A pdb=" N PHE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 541 " --> pdb=" O ILE C 537 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 137 through 139 removed outlier: 3.758A pdb=" N TYR B 137 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 139 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 144 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.563A pdb=" N GLU B 422 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 494 " --> pdb=" O GLU B 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 424 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS B 492 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS B 445 " --> pdb=" O ARG B 493 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 495 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 443 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 497 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 441 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 485 through 487 removed outlier: 3.599A pdb=" N GLU B 449 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY B 452 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE B 461 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 494 through 498 Processing sheet with id= E, first strand: chain 'A' and resid 463 through 465 removed outlier: 3.502A pdb=" N ALA A 463 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU A 449 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL A 488 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 137 through 139 removed outlier: 3.759A pdb=" N TYR D 137 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP D 139 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 144 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.563A pdb=" N GLU D 422 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 494 " --> pdb=" O GLU D 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 424 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS D 492 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS D 445 " --> pdb=" O ARG D 493 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU D 495 " --> pdb=" O VAL D 443 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL D 443 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 497 " --> pdb=" O TYR D 441 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR D 441 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 485 through 487 removed outlier: 3.600A pdb=" N GLU D 449 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY D 452 " --> pdb=" O ILE D 461 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE D 461 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 494 through 498 Processing sheet with id= J, first strand: chain 'C' and resid 463 through 465 removed outlier: 3.502A pdb=" N ALA C 463 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU C 449 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL C 488 " --> pdb=" O GLU C 449 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 1971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2302 1.30 - 1.43: 4363 1.43 - 1.56: 8865 1.56 - 1.69: 8 1.69 - 1.82: 156 Bond restraints: 15694 Sorted by residual: bond pdb=" C ASN A 355 " pdb=" O ASN A 355 " ideal model delta sigma weight residual 1.235 1.310 -0.075 1.26e-02 6.30e+03 3.52e+01 bond pdb=" C ASN C 355 " pdb=" O ASN C 355 " ideal model delta sigma weight residual 1.235 1.309 -0.074 1.26e-02 6.30e+03 3.45e+01 bond pdb=" C SER A 331 " pdb=" O SER A 331 " ideal model delta sigma weight residual 1.235 1.170 0.065 1.32e-02 5.74e+03 2.40e+01 bond pdb=" C SER C 331 " pdb=" O SER C 331 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.32e-02 5.74e+03 2.35e+01 bond pdb=" C GLN A 359 " pdb=" O GLN A 359 " ideal model delta sigma weight residual 1.236 1.290 -0.053 1.15e-02 7.56e+03 2.15e+01 ... (remaining 15689 not shown) Histogram of bond angle deviations from ideal: 95.24 - 103.03: 101 103.03 - 110.83: 5052 110.83 - 118.62: 7273 118.62 - 126.42: 8522 126.42 - 134.21: 186 Bond angle restraints: 21134 Sorted by residual: angle pdb=" N ASN A 348 " pdb=" CA ASN A 348 " pdb=" C ASN A 348 " ideal model delta sigma weight residual 112.23 101.94 10.29 1.26e+00 6.30e-01 6.67e+01 angle pdb=" N ASN C 348 " pdb=" CA ASN C 348 " pdb=" C ASN C 348 " ideal model delta sigma weight residual 112.23 101.96 10.27 1.26e+00 6.30e-01 6.65e+01 angle pdb=" N LEU D 226 " pdb=" CA LEU D 226 " pdb=" C LEU D 226 " ideal model delta sigma weight residual 113.72 104.00 9.72 1.30e+00 5.92e-01 5.60e+01 angle pdb=" N LYS C 332 " pdb=" CA LYS C 332 " pdb=" C LYS C 332 " ideal model delta sigma weight residual 111.14 103.08 8.06 1.08e+00 8.57e-01 5.58e+01 angle pdb=" N LYS A 332 " pdb=" CA LYS A 332 " pdb=" C LYS A 332 " ideal model delta sigma weight residual 111.14 103.10 8.04 1.08e+00 8.57e-01 5.54e+01 ... (remaining 21129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7694 17.75 - 35.50: 1141 35.50 - 53.25: 408 53.25 - 71.00: 91 71.00 - 88.75: 22 Dihedral angle restraints: 9356 sinusoidal: 3958 harmonic: 5398 Sorted by residual: dihedral pdb=" CA GLU D 112 " pdb=" C GLU D 112 " pdb=" N ASN D 113 " pdb=" CA ASN D 113 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLU B 112 " pdb=" C GLU B 112 " pdb=" N ASN B 113 " pdb=" CA ASN B 113 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C CYS D 228 " pdb=" N CYS D 228 " pdb=" CA CYS D 228 " pdb=" CB CYS D 228 " ideal model delta harmonic sigma weight residual -122.60 -131.35 8.75 0 2.50e+00 1.60e-01 1.23e+01 ... (remaining 9353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1916 0.061 - 0.121: 331 0.121 - 0.182: 52 0.182 - 0.243: 22 0.243 - 0.304: 7 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA CYS D 228 " pdb=" N CYS D 228 " pdb=" C CYS D 228 " pdb=" CB CYS D 228 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASN C 350 " pdb=" N ASN C 350 " pdb=" C ASN C 350 " pdb=" CB ASN C 350 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ASN A 350 " pdb=" N ASN A 350 " pdb=" C ASN A 350 " pdb=" CB ASN A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2325 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 380 " -0.027 2.00e-02 2.50e+03 5.40e-02 2.92e+01 pdb=" C ASP C 380 " 0.094 2.00e-02 2.50e+03 pdb=" O ASP C 380 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE C 381 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 380 " 0.027 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C ASP A 380 " -0.093 2.00e-02 2.50e+03 pdb=" O ASP A 380 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE A 381 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 270 " 0.070 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 271 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.054 5.00e-02 4.00e+02 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 11 1.82 - 2.59: 204 2.59 - 3.36: 20969 3.36 - 4.13: 37984 4.13 - 4.90: 68954 Nonbonded interactions: 128122 Sorted by model distance: nonbonded pdb=" CG1 ILE A 360 " pdb=" CD1 ILE D 385 " model vdw 1.049 3.860 nonbonded pdb=" CG1 ILE A 360 " pdb=" CG1 ILE D 385 " model vdw 1.127 3.840 nonbonded pdb=" NH2 ARG A 345 " pdb=" OE1 GLU D 374 " model vdw 1.261 2.520 nonbonded pdb=" CD1 ILE B 385 " pdb=" CG1 ILE C 360 " model vdw 1.395 3.860 nonbonded pdb=" CD1 ILE A 360 " pdb=" CG1 ILE D 385 " model vdw 1.405 3.860 ... (remaining 128117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A)) or resid 904)) selection = (chain 'B' and (resid 73 through 452 or resid 462 through 525 or resid 901 or (r \ esid 902 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C2A)) or resid 903)) selection = (chain 'C' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A)) or resid 904)) selection = (chain 'D' and (resid 73 through 452 or resid 462 through 525 or resid 901 or (r \ esid 902 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C2A)) or resid 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.010 Extract box with map and model: 5.440 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.210 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 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 : 0.006 0.102 15694 Z= 0.375 Angle : 0.838 17.910 21134 Z= 0.532 Chirality : 0.053 0.304 2328 Planarity : 0.006 0.100 2592 Dihedral : 19.522 88.748 5888 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.24 % Favored : 93.04 % Rotamer: Outliers : 5.09 % Allowed : 27.30 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1810 helix: -0.98 (0.16), residues: 1040 sheet: -0.97 (0.97), residues: 34 loop : -0.12 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 171 HIS 0.004 0.001 HIS C 295 PHE 0.030 0.002 PHE D 223 TYR 0.013 0.001 TYR B 237 ARG 0.004 0.000 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 235 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 ILE cc_start: 0.5216 (OUTLIER) cc_final: 0.4568 (tp) REVERT: B 377 VAL cc_start: 0.6841 (OUTLIER) cc_final: 0.6438 (t) REVERT: B 468 ASP cc_start: 0.5185 (t0) cc_final: 0.4528 (t0) REVERT: A 145 MET cc_start: 0.6947 (tpp) cc_final: 0.6686 (tpp) REVERT: A 351 LYS cc_start: 0.3960 (OUTLIER) cc_final: 0.3589 (mttp) REVERT: A 365 ARG cc_start: 0.0571 (OUTLIER) cc_final: 0.0045 (ttp-170) REVERT: D 128 ASP cc_start: 0.7860 (t0) cc_final: 0.7659 (t70) REVERT: D 468 ASP cc_start: 0.5363 (t0) cc_final: 0.5022 (t0) REVERT: C 183 GLU cc_start: 0.5865 (tm-30) cc_final: 0.5435 (tt0) REVERT: C 365 ARG cc_start: 0.1331 (OUTLIER) cc_final: 0.0286 (ttp-170) REVERT: C 369 GLU cc_start: 0.2964 (OUTLIER) cc_final: 0.2512 (pt0) outliers start: 83 outliers final: 31 residues processed: 306 average time/residue: 0.3123 time to fit residues: 135.7960 Evaluate side-chains 227 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 367 GLN Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 40.0000 chunk 141 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN D 295 HIS D 312 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15694 Z= 0.228 Angle : 0.628 13.136 21134 Z= 0.326 Chirality : 0.043 0.177 2328 Planarity : 0.005 0.067 2592 Dihedral : 11.729 93.799 2360 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.52 % Favored : 93.92 % Rotamer: Outliers : 4.66 % Allowed : 25.95 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1810 helix: -0.37 (0.16), residues: 1078 sheet: -0.37 (0.90), residues: 40 loop : 0.05 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 92 HIS 0.005 0.001 HIS C 295 PHE 0.025 0.002 PHE D 281 TYR 0.022 0.001 TYR A 368 ARG 0.007 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 209 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7136 (mmp) cc_final: 0.6311 (mmm) REVERT: B 128 ASP cc_start: 0.7787 (t0) cc_final: 0.7576 (t70) REVERT: B 152 ILE cc_start: 0.5118 (OUTLIER) cc_final: 0.4484 (tp) REVERT: B 218 ILE cc_start: 0.6367 (OUTLIER) cc_final: 0.5452 (tt) REVERT: A 89 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8272 (tp) REVERT: A 145 MET cc_start: 0.7174 (tpp) cc_final: 0.6946 (tpp) REVERT: A 344 MET cc_start: 0.4954 (mmt) cc_final: 0.3912 (pmm) REVERT: A 369 GLU cc_start: 0.1222 (OUTLIER) cc_final: 0.0443 (pt0) REVERT: A 393 LEU cc_start: 0.7462 (tp) cc_final: 0.6976 (pp) REVERT: D 342 ASP cc_start: 0.7051 (p0) cc_final: 0.6759 (p0) REVERT: C 89 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7572 (tp) REVERT: C 205 MET cc_start: 0.7039 (ttt) cc_final: 0.6831 (ttt) REVERT: C 221 LEU cc_start: 0.7880 (mm) cc_final: 0.7517 (mt) REVERT: C 369 GLU cc_start: 0.2712 (OUTLIER) cc_final: 0.2257 (pt0) outliers start: 76 outliers final: 31 residues processed: 268 average time/residue: 0.2545 time to fit residues: 103.9697 Evaluate side-chains 221 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 111 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 131 optimal weight: 30.0000 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15694 Z= 0.177 Angle : 0.573 11.351 21134 Z= 0.292 Chirality : 0.042 0.173 2328 Planarity : 0.004 0.057 2592 Dihedral : 10.055 81.852 2305 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.36 % Favored : 94.09 % Rotamer: Outliers : 3.93 % Allowed : 25.77 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1810 helix: 0.09 (0.16), residues: 1066 sheet: -1.05 (0.69), residues: 60 loop : 0.02 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 171 HIS 0.003 0.001 HIS C 295 PHE 0.017 0.001 PHE D 281 TYR 0.015 0.001 TYR D 237 ARG 0.009 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 210 time to evaluate : 1.570 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 87 MET cc_start: 0.7182 (mmp) cc_final: 0.6341 (mmm) REVERT: B 152 ILE cc_start: 0.5116 (OUTLIER) cc_final: 0.4910 (tt) REVERT: B 218 ILE cc_start: 0.6396 (OUTLIER) cc_final: 0.5625 (tt) REVERT: A 89 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8270 (tp) REVERT: A 126 LEU cc_start: 0.6243 (mt) cc_final: 0.5762 (mt) REVERT: A 322 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7092 (m-40) REVERT: A 344 MET cc_start: 0.4509 (mmt) cc_final: 0.3899 (pmm) REVERT: A 364 LEU cc_start: 0.3764 (OUTLIER) cc_final: 0.3532 (tm) REVERT: A 369 GLU cc_start: 0.2124 (OUTLIER) cc_final: 0.1779 (pt0) REVERT: A 393 LEU cc_start: 0.7509 (tp) cc_final: 0.7112 (pp) REVERT: D 128 ASP cc_start: 0.7848 (t0) cc_final: 0.7512 (t0) REVERT: C 89 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7710 (tp) REVERT: C 106 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: C 221 LEU cc_start: 0.7891 (mm) cc_final: 0.7453 (mt) REVERT: C 369 GLU cc_start: 0.3978 (OUTLIER) cc_final: 0.3406 (pt0) REVERT: C 503 MET cc_start: 0.7798 (ppp) cc_final: 0.6459 (ppp) outliers start: 64 outliers final: 25 residues processed: 262 average time/residue: 0.2638 time to fit residues: 105.8507 Evaluate side-chains 211 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 164 optimal weight: 0.4980 chunk 173 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15694 Z= 0.188 Angle : 0.567 10.362 21134 Z= 0.291 Chirality : 0.042 0.148 2328 Planarity : 0.004 0.052 2592 Dihedral : 9.383 75.375 2299 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.25 % Favored : 94.20 % Rotamer: Outliers : 3.62 % Allowed : 26.38 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1810 helix: 0.25 (0.16), residues: 1064 sheet: -1.01 (0.70), residues: 60 loop : -0.01 (0.27), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 171 HIS 0.005 0.001 HIS C 295 PHE 0.035 0.001 PHE C 336 TYR 0.014 0.001 TYR B 346 ARG 0.004 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 200 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.5703 (tt) REVERT: B 344 MET cc_start: 0.5676 (mmm) cc_final: 0.5464 (mmt) REVERT: A 89 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8294 (tp) REVERT: A 319 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7613 (tt) REVERT: A 322 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7056 (m-40) REVERT: A 365 ARG cc_start: 0.1964 (OUTLIER) cc_final: 0.1069 (ttp-170) REVERT: A 393 LEU cc_start: 0.7460 (tp) cc_final: 0.7118 (pp) REVERT: A 410 GLU cc_start: 0.6392 (pm20) cc_final: 0.6085 (mt-10) REVERT: D 128 ASP cc_start: 0.7900 (t0) cc_final: 0.7524 (t0) REVERT: D 421 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5637 (tt0) REVERT: C 89 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7802 (tp) REVERT: C 221 LEU cc_start: 0.7898 (mm) cc_final: 0.7421 (mt) REVERT: C 369 GLU cc_start: 0.4263 (OUTLIER) cc_final: 0.3747 (pt0) outliers start: 59 outliers final: 31 residues processed: 247 average time/residue: 0.2534 time to fit residues: 98.6010 Evaluate side-chains 223 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 HIS ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15694 Z= 0.435 Angle : 0.675 9.680 21134 Z= 0.351 Chirality : 0.047 0.201 2328 Planarity : 0.005 0.048 2592 Dihedral : 9.436 72.239 2287 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.30 % Favored : 94.14 % Rotamer: Outliers : 5.03 % Allowed : 26.26 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1810 helix: -0.16 (0.15), residues: 1074 sheet: -1.37 (0.67), residues: 60 loop : -0.15 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 171 HIS 0.009 0.001 HIS A 295 PHE 0.023 0.002 PHE B 236 TYR 0.040 0.002 TYR A 82 ARG 0.006 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 186 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7367 (mmp) cc_final: 0.6479 (mmm) REVERT: B 89 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.6804 (tp) REVERT: B 218 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.5725 (tt) REVERT: A 89 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8376 (tp) REVERT: A 365 ARG cc_start: 0.2533 (OUTLIER) cc_final: 0.1776 (ttp-170) REVERT: A 393 LEU cc_start: 0.7697 (tp) cc_final: 0.7292 (pp) REVERT: D 87 MET cc_start: 0.7172 (mmp) cc_final: 0.6238 (mmm) REVERT: D 89 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7030 (tp) REVERT: D 218 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.5729 (tt) REVERT: C 89 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8216 (tp) REVERT: C 344 MET cc_start: 0.5576 (mpt) cc_final: 0.5209 (mmt) REVERT: C 410 GLU cc_start: 0.6527 (pm20) cc_final: 0.6035 (mt-10) outliers start: 82 outliers final: 48 residues processed: 251 average time/residue: 0.2457 time to fit residues: 95.4738 Evaluate side-chains 228 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 173 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 0.4980 chunk 34 optimal weight: 30.0000 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15694 Z= 0.208 Angle : 0.586 11.531 21134 Z= 0.298 Chirality : 0.043 0.169 2328 Planarity : 0.004 0.048 2592 Dihedral : 8.547 60.438 2284 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.58 % Favored : 93.87 % Rotamer: Outliers : 3.87 % Allowed : 27.55 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1810 helix: 0.03 (0.15), residues: 1068 sheet: -1.34 (0.69), residues: 60 loop : -0.21 (0.26), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 171 HIS 0.005 0.001 HIS C 295 PHE 0.020 0.002 PHE D 281 TYR 0.025 0.001 TYR A 82 ARG 0.003 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 190 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7213 (mmp) cc_final: 0.6338 (mmm) REVERT: B 218 ILE cc_start: 0.6486 (OUTLIER) cc_final: 0.5193 (tt) REVERT: A 89 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8260 (tp) REVERT: A 217 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.6963 (mmm-85) REVERT: A 365 ARG cc_start: 0.2600 (OUTLIER) cc_final: 0.1829 (ttp-170) REVERT: A 393 LEU cc_start: 0.7546 (tp) cc_final: 0.7186 (pp) REVERT: D 87 MET cc_start: 0.7184 (mmp) cc_final: 0.6272 (mmm) REVERT: D 218 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.5661 (tt) REVERT: D 222 ILE cc_start: 0.8364 (tt) cc_final: 0.7897 (tp) REVERT: C 89 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8269 (tp) REVERT: C 126 LEU cc_start: 0.6630 (mt) cc_final: 0.6213 (mt) REVERT: C 217 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6789 (mmm-85) REVERT: C 221 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7484 (mt) REVERT: C 344 MET cc_start: 0.5386 (mpt) cc_final: 0.4996 (mmt) REVERT: C 410 GLU cc_start: 0.6400 (pm20) cc_final: 0.6137 (mt-10) outliers start: 63 outliers final: 42 residues processed: 234 average time/residue: 0.2410 time to fit residues: 87.8185 Evaluate side-chains 231 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 181 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 99 optimal weight: 0.1980 chunk 127 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 108 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15694 Z= 0.176 Angle : 0.572 11.784 21134 Z= 0.290 Chirality : 0.042 0.158 2328 Planarity : 0.004 0.048 2592 Dihedral : 8.157 60.282 2282 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.41 % Favored : 94.09 % Rotamer: Outliers : 3.62 % Allowed : 28.16 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1810 helix: 0.20 (0.16), residues: 1058 sheet: -1.22 (0.71), residues: 60 loop : -0.25 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 171 HIS 0.004 0.000 HIS A 295 PHE 0.020 0.001 PHE D 281 TYR 0.020 0.001 TYR A 82 ARG 0.006 0.000 ARG C 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 190 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7154 (mmp) cc_final: 0.6266 (mmm) REVERT: B 89 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.6761 (tp) REVERT: B 218 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.5215 (tt) REVERT: A 89 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8280 (tp) REVERT: A 217 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6836 (mmm-85) REVERT: A 365 ARG cc_start: 0.2410 (OUTLIER) cc_final: 0.1702 (ttp-170) REVERT: A 393 LEU cc_start: 0.7463 (tp) cc_final: 0.7174 (pp) REVERT: D 87 MET cc_start: 0.7106 (mmp) cc_final: 0.6201 (mmm) REVERT: D 89 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.6660 (tp) REVERT: D 218 ILE cc_start: 0.6540 (OUTLIER) cc_final: 0.5638 (tt) REVERT: C 126 LEU cc_start: 0.6614 (mt) cc_final: 0.6166 (mt) REVERT: C 217 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6773 (mmm-85) REVERT: C 221 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7417 (mt) REVERT: C 344 MET cc_start: 0.5322 (mpt) cc_final: 0.4975 (mpt) outliers start: 59 outliers final: 41 residues processed: 234 average time/residue: 0.2551 time to fit residues: 92.2233 Evaluate side-chains 231 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 181 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15694 Z= 0.195 Angle : 0.579 11.103 21134 Z= 0.294 Chirality : 0.042 0.159 2328 Planarity : 0.004 0.048 2592 Dihedral : 8.077 59.847 2282 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.41 % Favored : 94.03 % Rotamer: Outliers : 3.80 % Allowed : 27.98 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1810 helix: 0.30 (0.16), residues: 1060 sheet: -1.18 (0.71), residues: 60 loop : -0.20 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 92 HIS 0.005 0.001 HIS C 295 PHE 0.023 0.001 PHE A 539 TYR 0.055 0.001 TYR C 368 ARG 0.004 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 193 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7161 (mmp) cc_final: 0.6291 (mmm) REVERT: B 89 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.6769 (tp) REVERT: B 218 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.5211 (tt) REVERT: A 89 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8289 (tp) REVERT: A 217 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6854 (mmm-85) REVERT: A 340 MET cc_start: 0.4312 (mmm) cc_final: 0.3399 (mtp) REVERT: A 365 ARG cc_start: 0.2675 (OUTLIER) cc_final: 0.2324 (ttp-170) REVERT: A 393 LEU cc_start: 0.7473 (tp) cc_final: 0.7199 (pp) REVERT: D 87 MET cc_start: 0.7118 (mmp) cc_final: 0.6150 (mmm) REVERT: D 89 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.6569 (tp) REVERT: D 199 ILE cc_start: 0.8183 (tp) cc_final: 0.7915 (tp) REVERT: D 218 ILE cc_start: 0.6429 (OUTLIER) cc_final: 0.5027 (tt) REVERT: C 126 LEU cc_start: 0.6633 (mt) cc_final: 0.6196 (mt) REVERT: C 217 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6779 (mmm-85) REVERT: C 221 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7433 (mt) REVERT: C 344 MET cc_start: 0.5585 (mpt) cc_final: 0.5137 (mmt) outliers start: 62 outliers final: 40 residues processed: 236 average time/residue: 0.2502 time to fit residues: 91.2978 Evaluate side-chains 233 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15694 Z= 0.194 Angle : 0.583 10.271 21134 Z= 0.294 Chirality : 0.043 0.162 2328 Planarity : 0.004 0.052 2592 Dihedral : 7.959 59.927 2278 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.19 % Favored : 94.25 % Rotamer: Outliers : 3.50 % Allowed : 27.55 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1810 helix: 0.33 (0.16), residues: 1064 sheet: -1.23 (0.70), residues: 60 loop : -0.20 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 171 HIS 0.005 0.001 HIS C 295 PHE 0.020 0.001 PHE D 281 TYR 0.045 0.001 TYR C 368 ARG 0.016 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 193 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7212 (mmp) cc_final: 0.6337 (mmm) REVERT: B 89 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.6756 (tp) REVERT: B 218 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.5809 (tt) REVERT: B 346 TYR cc_start: 0.4600 (OUTLIER) cc_final: 0.4282 (t80) REVERT: A 89 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8220 (tp) REVERT: A 217 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6921 (mmm-85) REVERT: A 306 MET cc_start: 0.8231 (mmp) cc_final: 0.8023 (mmm) REVERT: A 340 MET cc_start: 0.4480 (mmm) cc_final: 0.3724 (mtp) REVERT: A 365 ARG cc_start: 0.2355 (OUTLIER) cc_final: 0.1655 (ttp-170) REVERT: A 393 LEU cc_start: 0.7310 (tp) cc_final: 0.7020 (pp) REVERT: D 87 MET cc_start: 0.7234 (mmp) cc_final: 0.6277 (mmm) REVERT: D 199 ILE cc_start: 0.8250 (tp) cc_final: 0.8035 (tp) REVERT: D 218 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.5070 (tt) REVERT: D 222 ILE cc_start: 0.8267 (tt) cc_final: 0.7826 (tp) REVERT: D 286 MET cc_start: 0.8247 (tmm) cc_final: 0.7506 (ttp) REVERT: C 126 LEU cc_start: 0.6633 (mt) cc_final: 0.6048 (mt) REVERT: C 221 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7413 (mt) REVERT: C 306 MET cc_start: 0.7539 (mmt) cc_final: 0.7034 (mmp) REVERT: C 344 MET cc_start: 0.5571 (mpt) cc_final: 0.5026 (mmt) outliers start: 57 outliers final: 43 residues processed: 234 average time/residue: 0.2596 time to fit residues: 94.0860 Evaluate side-chains 241 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 190 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 81 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 142 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15694 Z= 0.198 Angle : 0.588 11.395 21134 Z= 0.298 Chirality : 0.043 0.164 2328 Planarity : 0.004 0.055 2592 Dihedral : 7.927 59.468 2278 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.25 % Favored : 94.20 % Rotamer: Outliers : 3.44 % Allowed : 28.10 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1810 helix: 0.33 (0.16), residues: 1062 sheet: -1.21 (0.70), residues: 60 loop : -0.14 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 171 HIS 0.005 0.001 HIS C 295 PHE 0.018 0.001 PHE A 539 TYR 0.059 0.002 TYR A 368 ARG 0.013 0.000 ARG C 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 192 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7243 (mmp) cc_final: 0.6350 (mmm) REVERT: B 89 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.6762 (tp) REVERT: B 218 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.5797 (tt) REVERT: B 286 MET cc_start: 0.8229 (tmm) cc_final: 0.8028 (tmm) REVERT: B 346 TYR cc_start: 0.4619 (OUTLIER) cc_final: 0.4155 (t80) REVERT: A 89 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8291 (tp) REVERT: A 217 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.6946 (mmm-85) REVERT: A 306 MET cc_start: 0.8195 (mmp) cc_final: 0.7975 (mmp) REVERT: A 340 MET cc_start: 0.4624 (mmm) cc_final: 0.3816 (mtp) REVERT: A 365 ARG cc_start: 0.2502 (OUTLIER) cc_final: 0.2208 (ttp-170) REVERT: A 393 LEU cc_start: 0.7261 (tp) cc_final: 0.6983 (pp) REVERT: D 87 MET cc_start: 0.7257 (mmp) cc_final: 0.6256 (mmm) REVERT: D 89 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.6549 (tp) REVERT: D 199 ILE cc_start: 0.8270 (tp) cc_final: 0.8016 (tp) REVERT: D 218 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.4912 (tt) REVERT: C 217 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6805 (mmm-85) REVERT: C 306 MET cc_start: 0.7660 (mmt) cc_final: 0.7123 (mmp) REVERT: C 344 MET cc_start: 0.5348 (mpt) cc_final: 0.4847 (mmt) outliers start: 56 outliers final: 46 residues processed: 230 average time/residue: 0.2450 time to fit residues: 88.0839 Evaluate side-chains 243 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 188 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 346 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 0.0770 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.257489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.4018 r_free = 0.4018 target = 0.169975 restraints weight = 19021.848| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 4.68 r_work: 0.3682 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15694 Z= 0.172 Angle : 0.588 11.575 21134 Z= 0.296 Chirality : 0.043 0.208 2328 Planarity : 0.004 0.051 2592 Dihedral : 7.776 59.462 2278 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.14 % Favored : 94.42 % Rotamer: Outliers : 3.07 % Allowed : 28.59 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1810 helix: 0.38 (0.16), residues: 1064 sheet: -1.16 (0.71), residues: 60 loop : -0.11 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 92 HIS 0.004 0.000 HIS C 295 PHE 0.021 0.001 PHE D 115 TYR 0.044 0.001 TYR A 368 ARG 0.012 0.000 ARG C 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3442.76 seconds wall clock time: 64 minutes 3.93 seconds (3843.93 seconds total)