Starting phenix.real_space_refine on Fri Feb 16 01:13:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/02_2024/6ugf_20763_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/02_2024/6ugf_20763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/02_2024/6ugf_20763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/02_2024/6ugf_20763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/02_2024/6ugf_20763_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/02_2024/6ugf_20763_neut_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 4 5.21 5 S 63 5.16 5 C 8776 2.51 5 N 2430 2.21 5 O 2586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 244": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A ASP 387": "OD1" <-> "OD2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 295": "OD1" <-> "OD2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 295": "OD1" <-> "OD2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "E PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ARG 351": "NH1" <-> "NH2" Residue "E PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 194": "OD1" <-> "OD2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 431": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13874 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2231 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2273 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2297 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2318 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2306 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2186 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 13, 'TRANS': 297} Chain breaks: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 151 Chain: "G" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.76, per 1000 atoms: 0.56 Number of scatterers: 13874 At special positions: 0 Unit cell: (127.44, 139.32, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 15 15.00 Mg 4 11.99 O 2586 8.00 N 2430 7.00 C 8776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.7 seconds 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 8 sheets defined 40.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 175 through 181 removed outlier: 4.341A pdb=" N GLY A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 294 through 297 No H-bonds generated for 'chain 'A' and resid 294 through 297' Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 347 through 350 No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 364 through 374 removed outlier: 4.248A pdb=" N LYS A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 398 through 415 removed outlier: 4.280A pdb=" N VAL A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 172 through 180 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 366 through 374 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 401 through 415 removed outlier: 3.647A pdb=" N ARG B 415 " --> pdb=" O ASN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 434 Processing helix chain 'B' and resid 441 through 447 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 172 through 181 removed outlier: 3.805A pdb=" N GLN C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 211 through 214 No H-bonds generated for 'chain 'C' and resid 211 through 214' Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 272 through 284 Processing helix chain 'C' and resid 309 through 320 removed outlier: 4.442A pdb=" N LYS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 400 through 412 removed outlier: 4.767A pdb=" N VAL C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 433 Processing helix chain 'C' and resid 440 through 447 Processing helix chain 'C' and resid 457 through 469 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 172 through 181 removed outlier: 4.314A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 211 through 214 No H-bonds generated for 'chain 'D' and resid 211 through 214' Processing helix chain 'D' and resid 239 through 249 removed outlier: 3.577A pdb=" N ALA D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 284 Processing helix chain 'D' and resid 294 through 297 No H-bonds generated for 'chain 'D' and resid 294 through 297' Processing helix chain 'D' and resid 308 through 322 removed outlier: 4.678A pdb=" N ARG D 312 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 319 " --> pdb=" O GLU D 316 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 320 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET D 321 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP D 322 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 367 through 374 Processing helix chain 'D' and resid 386 through 392 Processing helix chain 'D' and resid 398 through 415 removed outlier: 4.249A pdb=" N ALA D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 433 No H-bonds generated for 'chain 'D' and resid 430 through 433' Processing helix chain 'D' and resid 440 through 449 removed outlier: 4.683A pdb=" N GLN D 448 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 removed outlier: 4.055A pdb=" N SER D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'E' and resid 199 through 206 Processing helix chain 'E' and resid 210 through 214 removed outlier: 3.695A pdb=" N LEU E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 210 through 214' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 241 through 248 Processing helix chain 'E' and resid 270 through 284 Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 364 through 374 Processing helix chain 'E' and resid 386 through 392 Processing helix chain 'E' and resid 400 through 415 removed outlier: 4.493A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 removed outlier: 3.861A pdb=" N LYS E 434 " --> pdb=" O MET E 430 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 430 through 435' Processing helix chain 'E' and resid 440 through 448 Processing helix chain 'E' and resid 457 through 468 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 174 through 181 removed outlier: 4.063A pdb=" N THR F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 194 No H-bonds generated for 'chain 'F' and resid 192 through 194' Processing helix chain 'F' and resid 199 through 206 Processing helix chain 'F' and resid 211 through 214 No H-bonds generated for 'chain 'F' and resid 211 through 214' Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 271 through 283 removed outlier: 3.655A pdb=" N ARG F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 297 No H-bonds generated for 'chain 'F' and resid 294 through 297' Processing helix chain 'F' and resid 311 through 320 Processing helix chain 'F' and resid 349 through 352 No H-bonds generated for 'chain 'F' and resid 349 through 352' Processing helix chain 'F' and resid 365 through 374 Processing helix chain 'F' and resid 386 through 391 Processing helix chain 'F' and resid 400 through 415 removed outlier: 4.344A pdb=" N LEU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 431 Processing helix chain 'F' and resid 440 through 447 Processing helix chain 'F' and resid 456 through 469 removed outlier: 3.537A pdb=" N ASP F 467 " --> pdb=" O LYS F 463 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.285A pdb=" N PHE A 334 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE A 291 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A 336 " --> pdb=" O ILE A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 230 through 233 Processing sheet with id= C, first strand: chain 'B' and resid 289 through 292 removed outlier: 3.895A pdb=" N ALA B 338 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 228 through 232 removed outlier: 6.301A pdb=" N VAL C 335 " --> pdb=" O MET C 229 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU C 231 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA C 337 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 338 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 228 through 232 removed outlier: 8.452A pdb=" N MET D 229 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL D 335 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU D 231 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA D 337 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER D 287 " --> pdb=" O PHE D 334 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU D 336 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE D 289 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ALA D 338 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE D 291 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 356 through 359 removed outlier: 6.554A pdb=" N VAL E 230 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE E 359 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA E 232 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER E 287 " --> pdb=" O PHE E 334 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU E 336 " --> pdb=" O SER E 287 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE E 289 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA E 338 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE E 291 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 230 through 233 Processing sheet with id= H, first strand: chain 'F' and resid 254 through 257 removed outlier: 6.459A pdb=" N ILE F 288 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL F 257 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE F 290 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE F 291 " --> pdb=" O LEU F 336 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 338 " --> pdb=" O ILE F 291 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1176 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: 3.24 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4485 1.34 - 1.45: 2238 1.45 - 1.57: 7269 1.57 - 1.69: 25 1.69 - 1.81: 109 Bond restraints: 14126 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.63e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.40e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.36e+01 ... (remaining 14121 not shown) Histogram of bond angle deviations from ideal: 98.52 - 106.38: 431 106.38 - 114.24: 8318 114.24 - 122.10: 7887 122.10 - 129.95: 2471 129.95 - 137.81: 86 Bond angle restraints: 19193 Sorted by residual: angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 115.98 23.89 1.00e+00 1.00e+00 5.71e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 113.58 23.25 1.00e+00 1.00e+00 5.41e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 116.67 23.20 1.00e+00 1.00e+00 5.38e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 118.32 21.55 1.00e+00 1.00e+00 4.64e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 115.32 21.51 1.00e+00 1.00e+00 4.62e+02 ... (remaining 19188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 7669 17.47 - 34.95: 747 34.95 - 52.42: 123 52.42 - 69.90: 24 69.90 - 87.37: 16 Dihedral angle restraints: 8579 sinusoidal: 3219 harmonic: 5360 Sorted by residual: dihedral pdb=" CA PRO A 362 " pdb=" C PRO A 362 " pdb=" N ASP A 363 " pdb=" CA ASP A 363 " ideal model delta harmonic sigma weight residual -180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA SER C 453 " pdb=" C SER C 453 " pdb=" N ALA C 454 " pdb=" CA ALA C 454 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLY A 305 " pdb=" C GLY A 305 " pdb=" N GLU A 306 " pdb=" CA GLU A 306 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 8576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1559 0.052 - 0.103: 546 0.103 - 0.155: 105 0.155 - 0.206: 15 0.206 - 0.258: 5 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C1' ATP B 501 " pdb=" C2' ATP B 501 " pdb=" N9 ATP B 501 " pdb=" O4' ATP B 501 " both_signs ideal model delta sigma weight residual False 2.41 2.67 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE B 341 " pdb=" CA ILE B 341 " pdb=" CG1 ILE B 341 " pdb=" CG2 ILE B 341 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 196 " pdb=" CA ILE A 196 " pdb=" CG1 ILE A 196 " pdb=" CG2 ILE A 196 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2227 not shown) Planarity restraints: 2443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 211 " -0.048 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO F 212 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO F 212 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 212 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 285 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.83e+00 pdb=" N PRO A 286 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 211 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO C 212 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.036 5.00e-02 4.00e+02 ... (remaining 2440 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 164 2.62 - 3.19: 11577 3.19 - 3.76: 20323 3.76 - 4.33: 26047 4.33 - 4.90: 42520 Nonbonded interactions: 100631 Sorted by model distance: nonbonded pdb=" O1G ATP E 501 " pdb="MG MG E 502 " model vdw 2.046 2.170 nonbonded pdb=" O3B ATP C 501 " pdb="MG MG C 502 " model vdw 2.050 2.170 nonbonded pdb=" O2G ATP B 501 " pdb="MG MG B 502 " model vdw 2.063 2.170 nonbonded pdb=" O2B ATP B 501 " pdb="MG MG B 502 " model vdw 2.069 2.170 nonbonded pdb=" O3G ATP D 501 " pdb="MG MG D 502 " model vdw 2.075 2.170 ... (remaining 100626 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 156 through 189 or (resid 190 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 216 or (resid 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 245 through 248 or \ (resid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 \ through 259 or (resid 260 and (name N or name CA or name C or name O or name CB \ )) or resid 261 through 294 or (resid 295 and (name N or name CA or name C or n \ ame O or name CB )) or resid 296 through 303 or (resid 304 and (name N or name C \ A or name C or name O or name CB )) or resid 305 through 322 or resid 332 throug \ h 343 or (resid 344 and (name N or name CA or name C or name O or name CB )) or \ resid 345 through 360 or (resid 361 and (name N or name CA or name C or name O o \ r name CB )) or resid 362 or (resid 363 and (name N or name CA or name C or name \ O or name CB )) or resid 364 through 366 or (resid 367 and (name N or name CA o \ r name C or name O or name CB )) or resid 368 or (resid 369 and (name N or name \ CA or name C or name O or name CB )) or resid 370 through 371 or (resid 372 thro \ ugh 373 and (name N or name CA or name C or name O or name CB )) or resid 374 or \ (resid 375 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 6 through 377 or (resid 378 and (name N or name CA or name C or name O or name C \ B )) or resid 379 or (resid 380 and (name N or name CA or name C or name O or na \ me CB )) or resid 381 or (resid 382 through 385 and (name N or name CA or name C \ or name O or name CB )) or resid 386 or (resid 387 through 394 and (name N or n \ ame CA or name C or name O or name CB )) or resid 395 through 399 or (resid 400 \ and (name N or name CA or name C or name O or name CB )) or resid 401 through 40 \ 5 or (resid 406 and (name N or name CA or name C or name O or name CB )) or resi \ d 407 through 413 or (resid 414 and (name N or name CA or name C or name O or na \ me CB )) or resid 415 through 417 or (resid 418 through 419 and (name N or name \ CA or name C or name O or name CB )) or resid 420 or (resid 421 through 422 and \ (name N or name CA or name C or name O or name CB )) or resid 423 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 8 or (resid 439 and (name N or name CA or name C or name O or name CB )) or resi \ d 440 through 443 or (resid 444 through 446 and (name N or name CA or name C or \ name O or name CB )) or resid 447 or (resid 448 through 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 through 457 or (resid 458 thro \ ugh 464 and (name N or name CA or name C or name O or name CB )) or resid 465 th \ rough 466 or (resid 467 through 468 and (name N or name CA or name C or name O o \ r name CB )) or resid 469 through 472)) selection = (chain 'B' and (resid 156 through 167 or (resid 168 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 182 or (resid 188 through 191 and (name N or name CA or name C or name \ O or name CB )) or resid 192 or (resid 193 through 194 and (name N or name CA o \ r name C or name O or name CB )) or resid 195 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 216 or (re \ sid 217 and (name N or name CA or name C or name O or name CB )) or resid 218 th \ rough 222 or (resid 223 and (name N or name CA or name C or name O or name CB )) \ or resid 224 through 226 or (resid 227 through 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 243 or (resid 244 and (nam \ e N or name CA or name C or name O or name CB or name CG )) or resid 245 through \ 248 or (resid 249 and (name N or name CA or name C or name O or name CB )) or r \ esid 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 through 268 or (resid 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 or (resid 271 and (name N or name CA or name C or n \ ame O or name CB )) or resid 272 through 278 or (resid 279 and (name N or name C \ A or name C or name O or name CB )) or resid 280 through 294 or (resid 295 and ( \ name N or name CA or name C or name O or name CB )) or resid 296 through 303 or \ (resid 304 and (name N or name CA or name C or name O or name CB )) or resid 305 \ or (resid 306 and (name N or name CA or name C or name O or name CB )) or resid \ 307 or (resid 308 through 309 and (name N or name CA or name C or name O or nam \ e CB )) or resid 310 through 314 or (resid 315 through 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 through 318 or (resid 319 and ( \ name N or name CA or name C or name O or name CB )) or resid 320 through 322 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 333 \ through 343 or (resid 344 and (name N or name CA or name C or name O or name CB \ )) or resid 345 or (resid 346 through 348 and (name N or name CA or name C or n \ ame O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 through 360 or (res \ id 361 and (name N or name CA or name C or name O or name CB )) or resid 362 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 through 387 or \ (resid 388 through 394 and (name N or name CA or name C or name O or name CB )) \ or resid 395 through 399 or (resid 400 and (name N or name CA or name C or name \ O or name CB )) or resid 401 through 405 or (resid 406 and (name N or name CA or \ name C or name O or name CB )) or resid 407 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 417 or (res \ id 418 through 419 and (name N or name CA or name C or name O or name CB )) or r \ esid 420 or (resid 421 through 422 and (name N or name CA or name C or name O or \ name CB )) or resid 423 through 430 or (resid 431 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 435 or (resid 436 t \ hrough 437 and (name N or name CA or name C or name O or name CB )) or resid 438 \ through 443 or (resid 444 through 446 and (name N or name CA or name C or name \ O or name CB )) or resid 447 or (resid 448 through 450 and (name N or name CA or \ name C or name O or name CB )) or resid 451 through 452 or (resid 453 through 4 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 455 through \ 457 or (resid 458 through 464 and (name N or name CA or name C or name O or nam \ e CB )) or resid 465 through 466 or (resid 467 through 468 and (name N or name C \ A or name C or name O or name CB )) or resid 469 through 471 or (resid 472 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 through 193 or (resid 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 222 or (resid 223 and (name N or name CA or name C or name O or na \ me CB )) or resid 224 through 229 or (resid 230 and (name N or name CA or name C \ or name O or name CB )) or resid 231 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 245 through 248 or \ (resid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 \ through 258 or (resid 259 through 260 and (name N or name CA or name C or name \ O or name CB )) or resid 261 through 268 or (resid 269 and (name N or name CA or \ name C or name O or name CB )) or resid 270 or (resid 271 and (name N or name C \ A or name C or name O or name CB )) or resid 272 through 278 or (resid 279 and ( \ name N or name CA or name C or name O or name CB )) or resid 280 through 294 or \ (resid 295 and (name N or name CA or name C or name O or name CB )) or resid 296 \ through 303 or (resid 304 and (name N or name CA or name C or name O or name CB \ )) or resid 305 or (resid 306 and (name N or name CA or name C or name O or nam \ e CB )) or resid 307 or (resid 308 through 309 and (name N or name CA or name C \ or name O or name CB )) or resid 310 through 314 or (resid 315 through 316 and ( \ name N or name CA or name C or name O or name CB )) or resid 317 through 318 or \ (resid 319 and (name N or name CA or name C or name O or name CB )) or resid 320 \ through 322 or (resid 332 and (name N or name CA or name C or name O or name CB \ )) or resid 333 through 343 or (resid 344 and (name N or name CA or name C or n \ ame O or name CB )) or resid 345 or (resid 346 through 348 and (name N or name C \ A or name C or name O or name CB )) or resid 349 through 354 or (resid 355 throu \ gh 356 and (name N or name CA or name C or name O or name CB )) or resid 357 thr \ ough 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) \ or resid 362 through 366 or (resid 367 and (name N or name CA or name C or name \ O or name CB )) or resid 368 or (resid 369 and (name N or name CA or name C or n \ ame O or name CB )) or resid 370 through 371 or (resid 372 through 373 and (name \ N or name CA or name C or name O or name CB )) or resid 374 or (resid 375 and ( \ name N or name CA or name C or name O or name CB )) or resid 376 through 377 or \ (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 and (name N or name CA or name C or name O or name CB )) or resid \ 381 through 382 or (resid 383 through 385 and (name N or name CA or name C or n \ ame O or name CB )) or resid 386 through 387 or (resid 388 through 394 and (name \ N or name CA or name C or name O or name CB )) or resid 395 through 405 or (res \ id 406 and (name N or name CA or name C or name O or name CB )) or resid 407 thr \ ough 413 or (resid 414 and (name N or name CA or name C or name O or name CB )) \ or resid 415 through 420 or (resid 421 through 422 and (name N or name CA or nam \ e C or name O or name CB )) or resid 423 through 430 or (resid 431 through 432 a \ nd (name N or name CA or name C or name O or name CB )) or resid 433 through 435 \ or (resid 436 through 437 and (name N or name CA or name C or name O or name CB \ )) or resid 438 or (resid 439 and (name N or name CA or name C or name O or nam \ e CB )) or resid 440 through 443 or (resid 444 through 446 and (name N or name C \ A or name C or name O or name CB )) or resid 447 or (resid 448 through 450 and ( \ name N or name CA or name C or name O or name CB )) or resid 451 through 452 or \ (resid 453 through 454 and (name N or name CA or name C or name O or name CB )) \ or resid 455 through 456 or (resid 457 through 464 and (name N or name CA or nam \ e C or name O or name CB )) or resid 465 through 467 or (resid 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 472)) selection = (chain 'D' and (resid 156 through 175 or (resid 176 through 177 and (name N or n \ ame CA or name C or name O or name CB )) or resid 178 through 189 or (resid 190 \ through 191 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 2 or (resid 193 through 194 and (name N or name CA or name C or name O or name C \ B )) or resid 195 through 199 or (resid 200 and (name N or name CA or name C or \ name O or name CB )) or resid 201 through 219 or (resid 220 and (name N or name \ CA or name C or name O or name CB )) or resid 221 through 222 or (resid 223 and \ (name N or name CA or name C or name O or name CB )) or resid 224 through 229 or \ (resid 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 243 or (resid 244 and (name N or name CA or name C or name O or name C \ B or name CG )) or resid 245 through 248 or (resid 249 and (name N or name CA or \ name C or name O or name CB )) or resid 250 or (resid 251 and (name N or name C \ A or name C or name O or name CB )) or resid 252 through 258 or (resid 259 throu \ gh 260 and (name N or name CA or name C or name O or name CB )) or resid 261 thr \ ough 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) \ or resid 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C or n \ ame O or name CB )) or resid 280 through 294 or (resid 295 and (name N or name C \ A or name C or name O or name CB )) or resid 296 through 303 or (resid 304 and ( \ name N or name CA or name C or name O or name CB )) or resid 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 or (resid 3 \ 08 through 309 and (name N or name CA or name C or name O or name CB )) or resid \ 310 through 314 or (resid 315 through 316 and (name N or name CA or name C or n \ ame O or name CB )) or resid 317 through 318 or (resid 319 and (name N or name C \ A or name C or name O or name CB )) or resid 320 through 322 or (resid 332 and ( \ name N or name CA or name C or name O or name CB )) or resid 333 through 343 or \ (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 345 \ through 346 or (resid 347 through 348 and (name N or name CA or name C or name \ O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name N o \ r name CA or name C or name O or name CB )) or resid 357 through 360 or (resid 3 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 362 or (res \ id 363 and (name N or name CA or name C or name O or name CB )) or resid 364 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 or (resid 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 381 or (resid 3 \ 82 through 385 and (name N or name CA or name C or name O or name CB )) or resid \ 386 or (resid 387 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 or (resid 421 through 422 and (name N or name CA or name C or n \ ame O or name CB )) or resid 423 through 430 or (resid 431 through 432 and (name \ N or name CA or name C or name O or name CB )) or resid 433 through 436 or (res \ id 437 and (name N or name CA or name C or name O or name CB )) or resid 438 or \ (resid 439 and (name N or name CA or name C or name O or name CB )) or resid 440 \ through 447 or (resid 448 through 450 and (name N or name CA or name C or name \ O or name CB )) or resid 451 through 457 or (resid 458 through 464 and (name N o \ r name CA or name C or name O or name CB )) or resid 465 through 467 or (resid 4 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 469 through \ 472)) selection = (chain 'E' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 216 or (resid 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 226 or (resid 227 \ through 228 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 9 or (resid 230 and (name N or name CA or name C or name O or name CB )) or resi \ d 231 through 243 or (resid 244 and (name N or name CA or name C or name O or na \ me CB or name CG )) or resid 245 through 248 or (resid 249 and (name N or name C \ A or name C or name O or name CB )) or resid 250 or (resid 251 and (name N or na \ me CA or name C or name O or name CB )) or resid 252 through 258 or (resid 259 t \ hrough 260 and (name N or name CA or name C or name O or name CB )) or resid 261 \ through 268 or (resid 269 and (name N or name CA or name C or name O or name CB \ )) or resid 270 or (resid 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C \ or name O or name CB )) or resid 280 through 294 or (resid 295 and (name N or na \ me CA or name C or name O or name CB )) or resid 296 through 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 through 314 \ or (resid 315 through 316 and (name N or name CA or name C or name O or name CB \ )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C or n \ ame O or name CB )) or resid 320 through 322 or (resid 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 343 or (resid 344 and ( \ name N or name CA or name C or name O or name CB )) or resid 345 through 346 or \ (resid 347 through 348 and (name N or name CA or name C or name O or name CB )) \ or resid 349 through 354 or (resid 355 through 356 and (name N or name CA or nam \ e C or name O or name CB )) or resid 357 through 360 or (resid 361 and (name N o \ r name CA or name C or name O or name CB )) or resid 362 through 366 or (resid 3 \ 67 and (name N or name CA or name C or name O or name CB )) or resid 368 or (res \ id 369 and (name N or name CA or name C or name O or name CB )) or resid 370 thr \ ough 371 or (resid 372 through 373 and (name N or name CA or name C or name O or \ name CB )) or resid 374 or (resid 375 and (name N or name CA or name C or name \ O or name CB )) or resid 376 through 377 or (resid 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 through 383 or (resid 384 through 3 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 386 through \ 388 or (resid 389 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 through 430 or (resid 431 through 432 and (name N or name CA or \ name C or name O or name CB )) or resid 433 through 436 or (resid 437 and (name \ N or name CA or name C or name O or name CB )) or resid 438 or (resid 439 and ( \ name N or name CA or name C or name O or name CB )) or resid 440 through 449 or \ (resid 450 and (name N or name CA or name C or name O or name CB )) or resid 451 \ through 452 or (resid 453 through 454 and (name N or name CA or name C or name \ O or name CB )) or resid 455 through 457 or (resid 458 through 464 and (name N o \ r name CA or name C or name O or name CB )) or resid 465 through 467 or (resid 4 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 469 through \ 472)) selection = (chain 'F' and (resid 156 through 170 or (resid 171 through 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 192 or (resid 193 through 194 and (name N or name CA or name C or name \ O or name CB )) or resid 195 through 219 or (resid 220 and (name N or name CA o \ r name C or name O or name CB )) or resid 221 through 222 or (resid 223 and (nam \ e N or name CA or name C or name O or name CB )) or resid 224 through 226 or (re \ sid 227 through 228 and (name N or name CA or name C or name O or name CB )) or \ resid 229 or (resid 230 and (name N or name CA or name C or name O or name CB )) \ or resid 231 through 258 or (resid 259 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 270 or (resid 271 and (name N \ or name CA or name C or name O or name CB )) or resid 272 through 303 or (resid \ 304 and (name N or name CA or name C or name O or name CB )) or resid 305 throug \ h 314 or (resid 315 through 316 and (name N or name CA or name C or name O or na \ me CB )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 322 or resid 332 through 345 or (r \ esid 346 through 348 and (name N or name CA or name C or name O or name CB )) or \ resid 349 through 354 or (resid 355 through 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 through 399 or (resid 400 and (name N or \ name CA or name C or name O or name CB )) or resid 401 through 417 or (resid 418 \ through 419 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 20 or (resid 421 through 422 and (name N or name CA or name C or name O or name \ CB )) or resid 423 through 430 or (resid 431 through 432 and (name N or name CA \ or name C or name O or name CB )) or resid 433 through 443 or (resid 444 through \ 446 and (name N or name CA or name C or name O or name CB )) or resid 447 or (r \ esid 448 through 450 and (name N or name CA or name C or name O or name CB )) or \ resid 451 through 452 or (resid 453 through 454 and (name N or name CA or name \ C or name O or name CB )) or resid 455 through 472)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 3.210 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 39.260 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 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 : 0.008 0.076 14126 Z= 0.509 Angle : 1.109 23.889 19193 Z= 0.767 Chirality : 0.054 0.258 2230 Planarity : 0.007 0.071 2443 Dihedral : 14.483 87.371 5093 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 0.30 % Allowed : 9.10 % Favored : 90.59 % 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: -4.55 (0.14), residues: 1826 helix: -3.10 (0.12), residues: 785 sheet: -2.15 (0.36), residues: 180 loop : -3.09 (0.16), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 226 HIS 0.006 0.001 HIS A 307 PHE 0.022 0.002 PHE C 353 TYR 0.019 0.002 TYR B 173 ARG 0.010 0.001 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 1.758 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 300 GLN cc_start: 0.8026 (tp40) cc_final: 0.7687 (mm110) REVERT: B 411 ASN cc_start: 0.9410 (t0) cc_final: 0.9149 (t0) REVERT: D 295 ASP cc_start: 0.8404 (p0) cc_final: 0.8128 (p0) REVERT: F 419 LYS cc_start: 0.6755 (mttp) cc_final: 0.6132 (mptt) outliers start: 4 outliers final: 0 residues processed: 182 average time/residue: 0.2612 time to fit residues: 69.2233 Evaluate side-chains 110 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0000 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN A 320 GLN A 340 ASN B 206 HIS B 307 HIS B 440 ASN D 203 GLN D 340 ASN ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14126 Z= 0.150 Angle : 0.519 9.803 19193 Z= 0.269 Chirality : 0.039 0.204 2230 Planarity : 0.004 0.052 2443 Dihedral : 9.716 89.096 2156 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.15 % Allowed : 3.31 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.17), residues: 1826 helix: -1.39 (0.17), residues: 788 sheet: -1.49 (0.37), residues: 186 loop : -2.65 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 343 HIS 0.003 0.001 HIS E 206 PHE 0.022 0.001 PHE F 317 TYR 0.007 0.001 TYR A 173 ARG 0.005 0.000 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 300 GLN cc_start: 0.7986 (tp40) cc_final: 0.7693 (mm110) REVERT: B 411 ASN cc_start: 0.9436 (t0) cc_final: 0.9113 (t0) REVERT: B 459 MET cc_start: 0.7423 (ptm) cc_final: 0.7167 (ppp) REVERT: C 229 MET cc_start: 0.8282 (tpt) cc_final: 0.7864 (tpp) REVERT: D 295 ASP cc_start: 0.8435 (p0) cc_final: 0.8069 (p0) REVERT: F 365 ASP cc_start: 0.8361 (p0) cc_final: 0.7850 (p0) REVERT: F 419 LYS cc_start: 0.6706 (mttp) cc_final: 0.6501 (mmtt) outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.2382 time to fit residues: 62.0765 Evaluate side-chains 110 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 0.0770 chunk 165 optimal weight: 0.0570 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN D 158 GLN ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14126 Z= 0.234 Angle : 0.545 10.038 19193 Z= 0.281 Chirality : 0.040 0.193 2230 Planarity : 0.004 0.051 2443 Dihedral : 9.520 88.578 2156 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: -2.16 (0.19), residues: 1826 helix: -0.64 (0.18), residues: 788 sheet: -1.30 (0.37), residues: 192 loop : -2.23 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 226 HIS 0.004 0.001 HIS C 307 PHE 0.014 0.001 PHE B 219 TYR 0.008 0.001 TYR E 284 ARG 0.005 0.000 ARG E 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7551 (mmm160) REVERT: B 411 ASN cc_start: 0.9472 (t0) cc_final: 0.9166 (t0) REVERT: B 459 MET cc_start: 0.7399 (ptm) cc_final: 0.6986 (ppp) REVERT: D 229 MET cc_start: 0.8879 (ttp) cc_final: 0.8633 (ttt) REVERT: D 295 ASP cc_start: 0.8379 (p0) cc_final: 0.8025 (p0) REVERT: E 194 ASP cc_start: 0.9113 (m-30) cc_final: 0.8660 (t70) REVERT: E 414 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8454 (ttm110) REVERT: F 419 LYS cc_start: 0.6803 (mttp) cc_final: 0.6554 (mmtt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2415 time to fit residues: 51.4086 Evaluate side-chains 99 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 177 optimal weight: 0.1980 chunk 87 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN B 158 GLN B 440 ASN E 320 GLN ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14126 Z= 0.223 Angle : 0.520 9.538 19193 Z= 0.267 Chirality : 0.040 0.135 2230 Planarity : 0.004 0.047 2443 Dihedral : 9.372 89.795 2156 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.19), residues: 1826 helix: -0.19 (0.19), residues: 789 sheet: -1.10 (0.37), residues: 191 loop : -2.11 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 343 HIS 0.004 0.001 HIS A 307 PHE 0.009 0.001 PHE C 353 TYR 0.008 0.001 TYR A 173 ARG 0.003 0.000 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.8014 (ptm160) cc_final: 0.7618 (mmm160) REVERT: B 411 ASN cc_start: 0.9451 (t0) cc_final: 0.9189 (t0) REVERT: B 459 MET cc_start: 0.7487 (ptm) cc_final: 0.7073 (ppp) REVERT: C 229 MET cc_start: 0.8401 (tpt) cc_final: 0.8180 (tpp) REVERT: D 229 MET cc_start: 0.8954 (ttp) cc_final: 0.8642 (ttt) REVERT: D 295 ASP cc_start: 0.8337 (p0) cc_final: 0.7990 (p0) REVERT: E 194 ASP cc_start: 0.9094 (m-30) cc_final: 0.8671 (t70) REVERT: E 414 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8450 (tpp80) REVERT: F 419 LYS cc_start: 0.6945 (mttp) cc_final: 0.6700 (mmtt) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.2418 time to fit residues: 51.9745 Evaluate side-chains 103 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14126 Z= 0.422 Angle : 0.683 9.872 19193 Z= 0.353 Chirality : 0.044 0.247 2230 Planarity : 0.004 0.043 2443 Dihedral : 9.964 86.304 2156 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.09 % 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: -1.62 (0.19), residues: 1826 helix: -0.17 (0.19), residues: 771 sheet: -1.10 (0.37), residues: 192 loop : -1.91 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 266 HIS 0.008 0.001 HIS A 307 PHE 0.023 0.002 PHE C 317 TYR 0.026 0.002 TYR E 284 ARG 0.004 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.8253 (ptm160) cc_final: 0.7958 (mmm160) REVERT: B 411 ASN cc_start: 0.9436 (t0) cc_final: 0.9233 (t0) REVERT: B 459 MET cc_start: 0.7709 (ptm) cc_final: 0.7160 (ppp) REVERT: C 203 GLN cc_start: 0.8590 (pp30) cc_final: 0.8338 (pp30) REVERT: C 303 ASN cc_start: 0.8330 (t0) cc_final: 0.8127 (t0) REVERT: D 229 MET cc_start: 0.9068 (ttp) cc_final: 0.8623 (ttt) REVERT: D 295 ASP cc_start: 0.8288 (p0) cc_final: 0.7987 (p0) REVERT: D 357 ILE cc_start: 0.9422 (mm) cc_final: 0.9166 (mt) REVERT: E 194 ASP cc_start: 0.9095 (m-30) cc_final: 0.8889 (t70) REVERT: F 419 LYS cc_start: 0.6927 (mttp) cc_final: 0.6266 (mmtm) REVERT: F 443 PHE cc_start: 0.8327 (m-80) cc_final: 0.7953 (m-80) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2513 time to fit residues: 48.8600 Evaluate side-chains 102 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 178 optimal weight: 30.0000 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN B 158 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14126 Z= 0.196 Angle : 0.536 9.965 19193 Z= 0.273 Chirality : 0.040 0.205 2230 Planarity : 0.004 0.066 2443 Dihedral : 9.415 89.978 2156 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.08 % Allowed : 1.58 % Favored : 98.34 % 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: -1.26 (0.20), residues: 1826 helix: 0.18 (0.19), residues: 785 sheet: -0.95 (0.37), residues: 187 loop : -1.78 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 226 HIS 0.003 0.001 HIS A 307 PHE 0.013 0.001 PHE C 317 TYR 0.014 0.001 TYR D 284 ARG 0.003 0.000 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.8186 (ptm160) cc_final: 0.7873 (mmm160) REVERT: B 411 ASN cc_start: 0.9420 (t0) cc_final: 0.9204 (t0) REVERT: B 459 MET cc_start: 0.7487 (ptm) cc_final: 0.7016 (ppp) REVERT: C 203 GLN cc_start: 0.8591 (pp30) cc_final: 0.8362 (pp30) REVERT: C 303 ASN cc_start: 0.8435 (t0) cc_final: 0.8185 (t0) REVERT: D 229 MET cc_start: 0.8924 (ttp) cc_final: 0.8526 (ttt) REVERT: D 295 ASP cc_start: 0.8345 (p0) cc_final: 0.7997 (p0) REVERT: E 414 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8403 (tpp80) REVERT: F 419 LYS cc_start: 0.6870 (mttp) cc_final: 0.6089 (mmtt) REVERT: F 443 PHE cc_start: 0.8394 (m-80) cc_final: 0.7994 (m-80) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.2279 time to fit residues: 46.7620 Evaluate side-chains 103 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS B 158 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14126 Z= 0.165 Angle : 0.503 9.806 19193 Z= 0.254 Chirality : 0.039 0.181 2230 Planarity : 0.003 0.054 2443 Dihedral : 9.067 88.380 2156 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1826 helix: 0.51 (0.19), residues: 785 sheet: -0.69 (0.39), residues: 181 loop : -1.63 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 226 HIS 0.003 0.001 HIS A 307 PHE 0.008 0.001 PHE C 317 TYR 0.015 0.001 TYR A 284 ARG 0.003 0.000 ARG E 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.7839 (tmm) cc_final: 0.7298 (ttt) REVERT: A 351 ARG cc_start: 0.8169 (ptm160) cc_final: 0.7915 (mmm160) REVERT: B 411 ASN cc_start: 0.9457 (t0) cc_final: 0.9234 (t0) REVERT: B 459 MET cc_start: 0.7493 (ptm) cc_final: 0.7068 (ppp) REVERT: C 303 ASN cc_start: 0.8506 (t0) cc_final: 0.8191 (t0) REVERT: D 229 MET cc_start: 0.8887 (ttp) cc_final: 0.8515 (ttt) REVERT: D 295 ASP cc_start: 0.8342 (p0) cc_final: 0.7983 (p0) REVERT: E 414 ARG cc_start: 0.8640 (mmm-85) cc_final: 0.8376 (tpp80) REVERT: F 419 LYS cc_start: 0.6940 (mttp) cc_final: 0.6238 (mmtt) REVERT: F 443 PHE cc_start: 0.8372 (m-80) cc_final: 0.7974 (m-80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2493 time to fit residues: 50.8759 Evaluate side-chains 109 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 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 158 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14126 Z= 0.127 Angle : 0.488 9.725 19193 Z= 0.243 Chirality : 0.038 0.172 2230 Planarity : 0.003 0.046 2443 Dihedral : 8.664 89.632 2156 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1826 helix: 0.75 (0.19), residues: 779 sheet: -0.42 (0.39), residues: 181 loop : -1.48 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 226 HIS 0.002 0.000 HIS A 307 PHE 0.015 0.001 PHE A 219 TYR 0.018 0.001 TYR C 284 ARG 0.004 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 MET cc_start: 0.7789 (tmm) cc_final: 0.7272 (ttt) REVERT: A 351 ARG cc_start: 0.8161 (ptm160) cc_final: 0.7893 (mmm160) REVERT: B 411 ASN cc_start: 0.9430 (t0) cc_final: 0.9208 (t0) REVERT: B 459 MET cc_start: 0.7540 (ptm) cc_final: 0.7167 (ppp) REVERT: C 303 ASN cc_start: 0.8511 (t0) cc_final: 0.8216 (t0) REVERT: D 229 MET cc_start: 0.8806 (ttp) cc_final: 0.8488 (ttt) REVERT: D 295 ASP cc_start: 0.8268 (p0) cc_final: 0.7862 (p0) REVERT: F 419 LYS cc_start: 0.6998 (mttp) cc_final: 0.6729 (mmtt) REVERT: F 443 PHE cc_start: 0.8330 (m-80) cc_final: 0.7950 (m-80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2392 time to fit residues: 53.8431 Evaluate side-chains 109 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 165 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN B 158 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14126 Z= 0.141 Angle : 0.496 9.595 19193 Z= 0.247 Chirality : 0.039 0.166 2230 Planarity : 0.003 0.044 2443 Dihedral : 8.517 89.832 2156 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.54 (0.20), residues: 1826 helix: 0.75 (0.19), residues: 788 sheet: -0.26 (0.39), residues: 181 loop : -1.45 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 226 HIS 0.002 0.000 HIS A 307 PHE 0.016 0.001 PHE E 317 TYR 0.033 0.001 TYR B 386 ARG 0.004 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: A 182 MET cc_start: 0.7701 (tmm) cc_final: 0.7153 (ttt) REVERT: A 351 ARG cc_start: 0.8160 (ptm160) cc_final: 0.7914 (mmm160) REVERT: B 411 ASN cc_start: 0.9459 (t0) cc_final: 0.9234 (t0) REVERT: B 459 MET cc_start: 0.7504 (ptm) cc_final: 0.7107 (ppp) REVERT: C 303 ASN cc_start: 0.8525 (t0) cc_final: 0.8235 (t0) REVERT: D 229 MET cc_start: 0.8798 (ttp) cc_final: 0.8472 (ttt) REVERT: D 295 ASP cc_start: 0.8276 (p0) cc_final: 0.7857 (p0) REVERT: F 198 MET cc_start: 0.8647 (pmm) cc_final: 0.8434 (pmm) REVERT: F 419 LYS cc_start: 0.7027 (mttp) cc_final: 0.6334 (mmtt) REVERT: F 443 PHE cc_start: 0.8317 (m-80) cc_final: 0.7955 (m-80) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2234 time to fit residues: 50.9075 Evaluate side-chains 106 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 0.0470 chunk 89 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14126 Z= 0.185 Angle : 0.517 9.524 19193 Z= 0.260 Chirality : 0.039 0.167 2230 Planarity : 0.003 0.044 2443 Dihedral : 8.541 89.794 2156 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.49 (0.20), residues: 1826 helix: 0.77 (0.19), residues: 790 sheet: -0.23 (0.40), residues: 181 loop : -1.39 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 266 HIS 0.003 0.001 HIS A 307 PHE 0.013 0.001 PHE C 317 TYR 0.026 0.001 TYR B 386 ARG 0.005 0.000 ARG E 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.843 Fit side-chains revert: symmetry clash REVERT: A 182 MET cc_start: 0.7685 (tmm) cc_final: 0.7156 (ttt) REVERT: A 351 ARG cc_start: 0.8186 (ptm160) cc_final: 0.7920 (mmm160) REVERT: B 411 ASN cc_start: 0.9465 (t0) cc_final: 0.9254 (t0) REVERT: B 459 MET cc_start: 0.7538 (ptm) cc_final: 0.7103 (ppp) REVERT: C 303 ASN cc_start: 0.8554 (t0) cc_final: 0.8203 (t0) REVERT: D 229 MET cc_start: 0.8832 (ttp) cc_final: 0.8499 (ttt) REVERT: D 295 ASP cc_start: 0.8176 (p0) cc_final: 0.7831 (p0) REVERT: F 419 LYS cc_start: 0.7025 (mttp) cc_final: 0.6342 (mmtt) REVERT: F 443 PHE cc_start: 0.8321 (m-80) cc_final: 0.7952 (m-80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2430 time to fit residues: 52.2710 Evaluate side-chains 107 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 134 optimal weight: 0.0000 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 61 optimal weight: 0.3980 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.076697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058425 restraints weight = 63329.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.059700 restraints weight = 36031.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.060652 restraints weight = 24549.348| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14126 Z= 0.158 Angle : 0.506 9.430 19193 Z= 0.253 Chirality : 0.039 0.161 2230 Planarity : 0.003 0.042 2443 Dihedral : 8.382 89.183 2156 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1826 helix: 0.80 (0.19), residues: 794 sheet: -0.19 (0.39), residues: 181 loop : -1.33 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 226 HIS 0.004 0.001 HIS F 206 PHE 0.012 0.001 PHE C 317 TYR 0.022 0.001 TYR B 386 ARG 0.005 0.000 ARG E 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.73 seconds wall clock time: 45 minutes 9.21 seconds (2709.21 seconds total)