Starting phenix.real_space_refine on Sat Mar 23 06:50:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/03_2024/7y5b_33615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/03_2024/7y5b_33615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/03_2024/7y5b_33615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/03_2024/7y5b_33615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/03_2024/7y5b_33615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/03_2024/7y5b_33615_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 17 5.49 5 Mg 5 5.21 5 S 106 5.16 5 C 22813 2.51 5 N 6242 2.21 5 O 6776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ASP 285": "OD1" <-> "OD2" Residue "E ASP 317": "OD1" <-> "OD2" Residue "F PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 313": "OD1" <-> "OD2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "a TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b GLU 86": "OE1" <-> "OE2" Residue "5 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35959 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3843 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 495} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3790 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 3822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3822 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 22, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 7, 'UNK:plan-1': 11, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3503 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3508 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3528 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2220 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "a" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1604 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1055 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 141} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "d" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3010 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 11, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 17, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 144 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "2" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 552 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "3" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 548 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "5" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "6" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "7" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "8" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 573 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 78} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "9" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "A" 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: "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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 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} Time building chain proxies: 18.45, per 1000 atoms: 0.51 Number of scatterers: 35959 At special positions: 0 Unit cell: (180.4, 123.2, 233.2, 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 106 16.00 P 17 15.00 Mg 5 11.99 O 6776 8.00 N 6242 7.00 C 22813 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: 14.31 Conformation dependent library (CDL) restraints added in 6.8 seconds 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 28 sheets defined 53.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.76 Creating SS restraints... Processing helix chain 'A' and resid 6 through 21 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.592A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 299 through 309 removed outlier: 4.095A pdb=" N PHE A 302 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 309 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.799A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 455 through 458 removed outlier: 4.400A pdb=" N SER A 458 " --> pdb=" O HIS A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.977A pdb=" N VAL A 464 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A 466 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.942A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 194 removed outlier: 4.090A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.613A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 removed outlier: 3.567A pdb=" N LEU B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 393 through 406 removed outlier: 4.392A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 464 through 477 Processing helix chain 'B' and resid 481 through 488 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.970A pdb=" N CYS C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.743A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.781A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE C 348 " --> pdb=" O ASN C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 431 removed outlier: 3.549A pdb=" N LEU C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 476 removed outlier: 4.881A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 466 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 467 " --> pdb=" O VAL C 464 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU C 472 " --> pdb=" O SER C 469 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL C 475 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 180 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 224 through 245 removed outlier: 5.355A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 269 Processing helix chain 'D' and resid 283 through 293 removed outlier: 4.647A pdb=" N ARG D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 326 removed outlier: 3.758A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 340 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 363 through 388 removed outlier: 4.541A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 418 through 423 removed outlier: 3.780A pdb=" N THR D 423 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 444 removed outlier: 4.400A pdb=" N LYS D 444 " --> pdb=" O ASP D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 449 removed outlier: 4.213A pdb=" N HIS D 449 " --> pdb=" O GLU D 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 446 through 449' Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 180 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.972A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 Processing helix chain 'E' and resid 284 through 293 removed outlier: 3.906A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.973A pdb=" N THR E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS E 326 " --> pdb=" O THR E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 363 through 386 removed outlier: 4.232A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 412 removed outlier: 4.381A pdb=" N LEU E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 412 " --> pdb=" O ILE E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 423 removed outlier: 4.693A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR E 423 " --> pdb=" O GLU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 446 through 449 removed outlier: 4.135A pdb=" N HIS E 449 " --> pdb=" O GLU E 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 446 through 449' Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 166 through 180 removed outlier: 4.121A pdb=" N ARG F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 209 through 212 Processing helix chain 'F' and resid 224 through 228 removed outlier: 3.525A pdb=" N MET F 228 " --> pdb=" O PRO F 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 224 through 228' Processing helix chain 'F' and resid 230 through 245 removed outlier: 3.653A pdb=" N GLU F 244 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 270 removed outlier: 3.714A pdb=" N LEU F 269 " --> pdb=" O GLU F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.087A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 363 through 388 removed outlier: 5.038A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 396 through 411 Processing helix chain 'F' and resid 417 through 420 Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 453 through 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'G' and resid 6 through 42 removed outlier: 3.998A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 59 Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.757A pdb=" N ASP G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 147 through 164 removed outlier: 4.142A pdb=" N GLY G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 228 through 301 Proline residue: G 237 - end of helix removed outlier: 3.809A pdb=" N LEU G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU G 249 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG G 261 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET G 263 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU G 273 " --> pdb=" O ASN G 269 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 100 Processing helix chain 'H' and resid 106 through 117 removed outlier: 3.815A pdb=" N LEU H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 52 removed outlier: 3.812A pdb=" N ALA a 51 " --> pdb=" O PHE a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 80 Processing helix chain 'a' and resid 89 through 108 removed outlier: 4.082A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 153 removed outlier: 3.989A pdb=" N ALA a 148 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG a 153 " --> pdb=" O GLY a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 163 Processing helix chain 'a' and resid 171 through 205 Proline residue: a 182 - end of helix Processing helix chain 'a' and resid 213 through 245 removed outlier: 3.622A pdb=" N THR a 220 " --> pdb=" O ALA a 216 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 47 removed outlier: 4.044A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 58 removed outlier: 4.221A pdb=" N LYS b 55 " --> pdb=" O PRO b 51 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL b 56 " --> pdb=" O PRO b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 60 through 146 removed outlier: 3.927A pdb=" N LEU b 64 " --> pdb=" O ARG b 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG b 72 " --> pdb=" O ALA b 68 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER b 74 " --> pdb=" O ASP b 70 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA b 75 " --> pdb=" O ASN b 71 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER b 134 " --> pdb=" O ASP b 130 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN b 139 " --> pdb=" O ALA b 135 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 160 Processing helix chain 'd' and resid 3 through 17 removed outlier: 4.131A pdb=" N ILE d 9 " --> pdb=" O ILE d 5 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY d 10 " --> pdb=" O GLY d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 55 removed outlier: 3.689A pdb=" N VAL d 26 " --> pdb=" O VAL d 22 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP d 55 " --> pdb=" O LEU d 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 57 through 135 Processing helix chain 'd' and resid 140 through 156 removed outlier: 4.057A pdb=" N SER d 144 " --> pdb=" O PRO d 140 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 190 Processing helix chain 'd' and resid 198 through 215 Processing helix chain 'd' and resid 218 through 223 Processing helix chain 'd' and resid 231 through 239 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 284 removed outlier: 4.136A pdb=" N VAL d 271 " --> pdb=" O LEU d 267 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU d 272 " --> pdb=" O ILE d 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 312 Processing helix chain 'd' and resid 322 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 371 Processing helix chain 'd' and resid 387 through 400 Processing helix chain 'd' and resid 432 through 441 Processing helix chain '1' and resid 7 through 45 removed outlier: 4.014A pdb=" N ALA 1 44 " --> pdb=" O ILE 1 40 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG 1 45 " --> pdb=" O SER 1 41 " (cutoff:3.500A) Processing helix chain '1' and resid 50 through 52 No H-bonds generated for 'chain '1' and resid 50 through 52' Processing helix chain '1' and resid 54 through 80 removed outlier: 3.781A pdb=" N VAL 1 64 " --> pdb=" O THR 1 60 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 45 Processing helix chain '2' and resid 51 through 78 removed outlier: 4.249A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '3' and resid 6 through 45 Processing helix chain '3' and resid 54 through 79 Processing helix chain '4' and resid 6 through 45 Processing helix chain '4' and resid 55 through 78 removed outlier: 3.999A pdb=" N ALA 4 67 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR 4 68 " --> pdb=" O VAL 4 64 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU 4 77 " --> pdb=" O ALA 4 73 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE 4 78 " --> pdb=" O PHE 4 74 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 44 removed outlier: 3.830A pdb=" N ILE 5 43 " --> pdb=" O LEU 5 39 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA 5 44 " --> pdb=" O ILE 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 54 through 80 Processing helix chain '6' and resid 7 through 43 Processing helix chain '6' and resid 54 through 80 removed outlier: 3.634A pdb=" N LEU 6 63 " --> pdb=" O ILE 6 59 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL 6 64 " --> pdb=" O THR 6 60 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 45 Processing helix chain '7' and resid 53 through 80 removed outlier: 3.569A pdb=" N PHE 7 57 " --> pdb=" O LEU 7 53 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 43 Processing helix chain '8' and resid 50 through 52 No H-bonds generated for 'chain '8' and resid 50 through 52' Processing helix chain '8' and resid 54 through 81 removed outlier: 3.988A pdb=" N LEU 8 63 " --> pdb=" O ILE 8 59 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL 8 64 " --> pdb=" O THR 8 60 " (cutoff:3.500A) Processing helix chain '9' and resid 7 through 45 removed outlier: 3.887A pdb=" N ALA 9 11 " --> pdb=" O ILE 9 8 " (cutoff:3.500A) Processing helix chain '9' and resid 54 through 80 Processing sheet with id= A, first strand: chain 'A' and resid 55 through 57 removed outlier: 4.104A pdb=" N GLY A 64 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 352 through 355 removed outlier: 7.307A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 171 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 204 through 209 removed outlier: 3.587A pdb=" N THR A 233 " --> pdb=" O CYS A 204 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.761A pdb=" N THR A 325 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 271 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 33 through 36 removed outlier: 6.782A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.665A pdb=" N GLU B 45 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 99 through 102 removed outlier: 3.646A pdb=" N ARG B 130 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 128 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.774A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 329 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.513A pdb=" N LYS C 92 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 36 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.691A pdb=" N THR C 128 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 170 through 172 removed outlier: 3.743A pdb=" N GLY C 172 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 232 through 237 removed outlier: 9.268A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.702A pdb=" N VAL D 20 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG D 63 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN D 55 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS D 47 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 87 through 90 Processing sheet with id= P, first strand: chain 'D' and resid 329 through 332 removed outlier: 3.591A pdb=" N ALA D 329 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 214 " --> pdb=" O SER D 185 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 19 through 23 removed outlier: 3.560A pdb=" N GLN E 55 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 47 " --> pdb=" O ILE E 40 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 87 through 90 Processing sheet with id= S, first strand: chain 'E' and resid 329 through 332 removed outlier: 7.412A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 213 through 215 removed outlier: 6.942A pdb=" N SER E 185 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU E 250 " --> pdb=" O VAL E 186 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 11 through 16 removed outlier: 3.864A pdb=" N VAL F 13 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS F 47 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE F 40 " --> pdb=" O LYS F 47 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 87 through 89 removed outlier: 3.610A pdb=" N VAL F 88 " --> pdb=" O TRP F 118 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP F 118 " --> pdb=" O VAL F 88 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 155 through 158 removed outlier: 8.274A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 76 through 81 removed outlier: 6.616A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 185 through 188 Processing sheet with id= Z, first strand: chain 'H' and resid 17 through 19 removed outlier: 3.880A pdb=" N ARG H 78 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER H 71 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 31 through 34 removed outlier: 3.613A pdb=" N THR H 25 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE H 34 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL H 23 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'd' and resid 408 through 411 removed outlier: 3.750A pdb=" N ALA d 381 " --> pdb=" O HIS d 410 " (cutoff:3.500A) 1918 hydrogen bonds defined for protein. 5412 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: 11.72 Time building geometry restraints manager: 15.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8329 1.33 - 1.45: 7032 1.45 - 1.57: 20978 1.57 - 1.69: 28 1.69 - 1.82: 192 Bond restraints: 36559 Sorted by residual: bond pdb=" N LYS D 95 " pdb=" CA LYS D 95 " ideal model delta sigma weight residual 1.458 1.476 -0.018 1.35e-02 5.49e+03 1.72e+00 bond pdb=" CD GLN d 86 " pdb=" OE1 GLN d 86 " ideal model delta sigma weight residual 1.231 1.209 0.022 1.90e-02 2.77e+03 1.31e+00 bond pdb=" CD GLU d 96 " pdb=" OE1 GLU d 96 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.29e+00 bond pdb=" CA ASP G 271 " pdb=" C ASP G 271 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.30e-02 5.92e+03 1.27e+00 bond pdb=" C THR G 267 " pdb=" O THR G 267 " ideal model delta sigma weight residual 1.237 1.250 -0.013 1.17e-02 7.31e+03 1.25e+00 ... (remaining 36554 not shown) Histogram of bond angle deviations from ideal: 97.39 - 105.89: 857 105.89 - 114.38: 21745 114.38 - 122.88: 24452 122.88 - 131.38: 2542 131.38 - 139.87: 45 Bond angle restraints: 49641 Sorted by residual: angle pdb=" N GLN d 86 " pdb=" CA GLN d 86 " pdb=" CB GLN d 86 " ideal model delta sigma weight residual 110.28 116.82 -6.54 1.55e+00 4.16e-01 1.78e+01 angle pdb=" C ALA d 95 " pdb=" N GLU d 96 " pdb=" CA GLU d 96 " ideal model delta sigma weight residual 120.72 114.24 6.48 1.67e+00 3.59e-01 1.50e+01 angle pdb=" N GLU d 96 " pdb=" CA GLU d 96 " pdb=" CB GLU d 96 " ideal model delta sigma weight residual 110.39 116.83 -6.44 1.66e+00 3.63e-01 1.50e+01 angle pdb=" C VAL D 94 " pdb=" N LYS D 95 " pdb=" CA LYS D 95 " ideal model delta sigma weight residual 123.47 129.17 -5.70 1.53e+00 4.27e-01 1.39e+01 angle pdb=" C ILE a 71 " pdb=" N GLN a 72 " pdb=" CA GLN a 72 " ideal model delta sigma weight residual 120.31 114.77 5.54 1.52e+00 4.33e-01 1.33e+01 ... (remaining 49636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.85: 20746 26.85 - 53.69: 1012 53.69 - 80.54: 104 80.54 - 107.38: 20 107.38 - 134.23: 1 Dihedral angle restraints: 21883 sinusoidal: 8258 harmonic: 13625 Sorted by residual: dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual 300.00 165.77 134.23 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" O2A ADP D 601 " pdb=" O3A ADP D 601 " pdb=" PA ADP D 601 " pdb=" PB ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 -134.32 74.32 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" CA ASP E 114 " pdb=" CB ASP E 114 " pdb=" CG ASP E 114 " pdb=" OD1 ASP E 114 " ideal model delta sinusoidal sigma weight residual -30.00 -87.80 57.80 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 21880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3899 0.032 - 0.064: 1292 0.064 - 0.097: 430 0.097 - 0.129: 187 0.129 - 0.161: 18 Chirality restraints: 5826 Sorted by residual: chirality pdb=" CA THR 1 55 " pdb=" N THR 1 55 " pdb=" C THR 1 55 " pdb=" CB THR 1 55 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA THR 3 55 " pdb=" N THR 3 55 " pdb=" C THR 3 55 " pdb=" CB THR 3 55 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA THR 2 55 " pdb=" N THR 2 55 " pdb=" C THR 2 55 " pdb=" CB THR 2 55 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.09e-01 ... (remaining 5823 not shown) Planarity restraints: 6454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 112 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.45e+00 pdb=" N PRO A 113 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY 9 29 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C GLY 9 29 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY 9 29 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE 9 30 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 9 32 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASP 9 32 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP 9 32 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY 9 33 " -0.013 2.00e-02 2.50e+03 ... (remaining 6451 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 157 2.49 - 3.09: 26195 3.09 - 3.70: 54322 3.70 - 4.30: 69806 4.30 - 4.90: 116199 Nonbonded interactions: 266679 Sorted by model distance: nonbonded pdb=" O1B ATP F 601 " pdb="MG MG F 602 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR F 167 " pdb="MG MG F 602 " model vdw 1.963 2.170 nonbonded pdb=" O3G ATP F 601 " pdb="MG MG F 602 " model vdw 1.980 2.170 nonbonded pdb=" O3A ATP B 601 " pdb="MG MG B 602 " model vdw 1.982 2.170 nonbonded pdb=" O1G ATP A 601 " pdb="MG MG A 602 " model vdw 1.984 2.170 ... (remaining 266674 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 '1' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '2' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 84)) selection = (chain '3' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '4' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '6' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '7' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '8' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '9' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) } ncs_group { reference = (chain 'A' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 132 or (resid 133 and (name N or name CA or name C or nam \ e O or name CB )) or resid 134 through 355 or (resid 356 and (name N or name CA \ or name C or name O or name CB )) or resid 357 or (resid 358 and (name N or name \ CA or name C or name O or name CB )) or resid 359 through 400 or (resid 401 thr \ ough 402 and (name N or name CA or name C or name O or name CB )) or resid 403 t \ hrough 411 or (resid 412 and (name N or name CA or name C or name O or name CB ) \ ) or resid 413 through 416 or (resid 417 through 419 and (name N or name CA or n \ ame C or name O or name CB )) or resid 420 through 461 or (resid 462 through 463 \ and (name N or name CA or name C or name O or name CB )) or resid 464 through 4 \ 67 or (resid 468 and (name N or name CA or name C or name O or name CB )) or res \ id 469 or (resid 470 and (name N or name CA or name C or name O or name CB )) or \ resid 471 through 494 or (resid 495 through 499 and (name N or name CA or name \ C or name O or name CB )) or resid 500 through 505 or (resid 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 through 516 or resid 518 \ through 520 or resid 601 through 602)) selection = (chain 'B' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 132 or (resid 133 and (name N or name CA or name C or nam \ e O or name CB )) or resid 134 through 190 or (resid 191 through 192 and (name N \ or name CA or name C or name O or name CB )) or resid 193 through 316 or (resid \ 317 through 318 and (name N or name CA or name C or name O or name CB )) or res \ id 319 through 355 or (resid 356 and (name N or name CA or name C or name O or n \ ame CB )) or resid 357 or (resid 358 and (name N or name CA or name C or name O \ or name CB )) or resid 359 through 401 or (resid 402 and (name N or name CA or n \ ame C or name O or name CB )) or resid 403 through 411 or (resid 412 and (name N \ or name CA or name C or name O or name CB )) or resid 413 through 416 or (resid \ 417 through 419 and (name N or name CA or name C or name O or name CB )) or res \ id 420 through 456 or (resid 457 and (name N or name CA or name C or name O or n \ ame CB )) or resid 458 through 467 or (resid 468 and (name N or name CA or name \ C or name O or name CB )) or resid 469 through 493 or (resid 494 through 499 and \ (name N or name CA or name C or name O or name CB )) or resid 500 through 505 o \ r (resid 506 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 07 through 516 or resid 518 through 520 or resid 601 through 602)) selection = (chain 'C' and (resid 29 through 190 or (resid 191 through 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 through 316 or (resid 317 t \ hrough 318 and (name N or name CA or name C or name O or name CB )) or resid 319 \ through 400 or (resid 401 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 403 through 456 or (resid 457 and (name N or name CA or \ name C or name O or name CB )) or resid 458 through 469 or (resid 470 and (name \ N or name CA or name C or name O or name CB )) or resid 471 through 493 or (res \ id 494 through 499 and (name N or name CA or name C or name O or name CB )) or r \ esid 500 through 516 or resid 537 through 538 or resid 540 or resid 601 through \ 602)) } ncs_group { reference = (chain 'D' and (resid 8 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB )) or resid 105 through 106 or (resid 107 and (name N or \ name CA or name C or name O or name CB )) or resid 108 through 198 or (resid 19 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 200 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 285 or (resid 286 and (name N or name CA or name C or name O or \ name CB )) or resid 287 through 362 or (resid 363 through 364 and (name N or nam \ e CA or name C or name O or name CB )) or resid 365 through 369 or (resid 370 th \ rough 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ through 380 or (resid 381 and (name N or name CA or name C or name O or name CB \ )) or resid 382 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 424 or (resid 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 through 471)) selection = (chain 'E' and (resid 8 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 220 or (resid 221 through 222 an \ d (name N or name CA or name C or name O or name CB )) or resid 223 through 284 \ or (resid 285 through 286 and (name N or name CA or name C or name O or name CB \ )) or resid 287 through 288 or (resid 289 and (name N or name CA or name C or na \ me O or name CB )) or resid 290 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 370 or (resid 371 and (n \ ame N or name CA or name C or name O or name CB )) or resid 372 through 395 or ( \ resid 396 through 398 and (name N or name CA or name C or name O or name CB )) o \ r resid 399 through 461 or (resid 462 and (name N or name CA or name C or name O \ or name CB )) or resid 463 through 465 or (resid 466 and (name N or name CA or \ name C or name O or name CB )) or resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB )) or resid 105 through 134 or (resid 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 198 or (resid 19 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 200 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 220 or (resid 221 through 222 and (name N or name CA or name C o \ r name O or name CB )) or resid 223 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 through 362 or (resid 363 th \ rough 364 and (name N or name CA or name C or name O or name CB )) or resid 365 \ through 369 or (resid 370 through 371 and (name N or name CA or name C or name O \ or name CB )) or resid 372 through 380 or (resid 381 and (name N or name CA or \ name C or name O or name CB )) or resid 382 through 383 or (resid 384 and (name \ N or name CA or name C or name O or name CB )) or resid 385 through 395 or (resi \ d 396 through 398 and (name N or name CA or name C or name O or name CB )) or re \ sid 399 through 402 or (resid 403 and (name N or name CA or name C or name O or \ name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA or name \ C or name O or name CB )) or resid 434 through 461 or (resid 462 and (name N or \ name CA or name C or name O or name CB )) or resid 463 through 465 or (resid 46 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 467 through \ 471)) } 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: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 18.550 Check model and map are aligned: 0.530 Set scattering table: 0.380 Process input model: 91.640 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36559 Z= 0.155 Angle : 0.557 9.140 49641 Z= 0.284 Chirality : 0.040 0.161 5826 Planarity : 0.004 0.058 6454 Dihedral : 15.008 134.229 13153 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.12), residues: 4784 helix: 2.12 (0.11), residues: 2490 sheet: 0.90 (0.24), residues: 484 loop : -1.01 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 218 HIS 0.005 0.001 HIS a 146 PHE 0.020 0.001 PHE 7 57 TYR 0.022 0.001 TYR a 145 ARG 0.007 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 15 ILE cc_start: 0.4093 (mt) cc_final: 0.3893 (mt) REVERT: 1 58 PHE cc_start: 0.7221 (m-10) cc_final: 0.7014 (m-10) REVERT: 3 75 MET cc_start: 0.6914 (tmm) cc_final: 0.6283 (tmm) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.4036 time to fit residues: 246.2025 Evaluate side-chains 260 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 404 optimal weight: 6.9990 chunk 363 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 375 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 434 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN a 229 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36559 Z= 0.179 Angle : 0.501 8.105 49641 Z= 0.252 Chirality : 0.039 0.229 5826 Planarity : 0.004 0.054 6454 Dihedral : 6.741 119.280 5333 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.12), residues: 4784 helix: 2.23 (0.11), residues: 2489 sheet: 0.82 (0.23), residues: 493 loop : -1.01 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 118 HIS 0.003 0.001 HIS C 259 PHE 0.015 0.001 PHE H 24 TYR 0.021 0.001 TYR a 145 ARG 0.004 0.000 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7595 (t0) cc_final: 0.7292 (t0) REVERT: A 229 MET cc_start: 0.8279 (tpp) cc_final: 0.8056 (tpp) REVERT: D 309 TYR cc_start: 0.8386 (t80) cc_final: 0.8086 (t80) REVERT: 1 9 ILE cc_start: 0.2168 (mt) cc_final: 0.1900 (mt) REVERT: 3 75 MET cc_start: 0.6931 (tmm) cc_final: 0.6199 (tmm) REVERT: 5 15 ILE cc_start: 0.5586 (mm) cc_final: 0.5310 (mm) REVERT: 5 75 MET cc_start: 0.6271 (pmm) cc_final: 0.5768 (pmm) REVERT: 9 70 ILE cc_start: 0.8425 (tp) cc_final: 0.8220 (tp) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.4054 time to fit residues: 247.3027 Evaluate side-chains 258 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 4.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 241 optimal weight: 3.9990 chunk 135 optimal weight: 0.0170 chunk 362 optimal weight: 4.9990 chunk 296 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 435 optimal weight: 20.0000 chunk 470 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 chunk 432 optimal weight: 10.0000 chunk 148 optimal weight: 0.0040 chunk 349 optimal weight: 0.9980 overall best weight: 0.7432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN a 229 GLN d 220 ASN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 36559 Z= 0.149 Angle : 0.500 10.453 49641 Z= 0.250 Chirality : 0.039 0.229 5826 Planarity : 0.004 0.049 6454 Dihedral : 6.492 111.093 5333 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.13), residues: 4784 helix: 2.24 (0.11), residues: 2497 sheet: 0.85 (0.23), residues: 492 loop : -1.00 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 118 HIS 0.004 0.001 HIS B 259 PHE 0.029 0.001 PHE E 324 TYR 0.020 0.001 TYR a 145 ARG 0.005 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 309 TYR cc_start: 0.8363 (t80) cc_final: 0.8144 (t80) REVERT: G 293 ILE cc_start: 0.8206 (tt) cc_final: 0.7992 (tt) REVERT: 1 9 ILE cc_start: 0.2264 (mt) cc_final: 0.1963 (mt) REVERT: 1 21 MET cc_start: 0.6932 (mmm) cc_final: 0.6385 (tpp) REVERT: 1 75 MET cc_start: 0.7859 (ppp) cc_final: 0.7619 (ppp) REVERT: 3 75 MET cc_start: 0.6898 (tmm) cc_final: 0.6280 (tmm) REVERT: 9 70 ILE cc_start: 0.8479 (tp) cc_final: 0.8226 (tp) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.4161 time to fit residues: 266.0586 Evaluate side-chains 262 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 430 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 226 optimal weight: 0.4980 chunk 48 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 437 optimal weight: 0.9980 chunk 463 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 414 optimal weight: 0.0040 chunk 124 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN D 175 ASN F 55 GLN a 229 GLN 6 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36559 Z= 0.136 Angle : 0.497 10.021 49641 Z= 0.248 Chirality : 0.039 0.234 5826 Planarity : 0.004 0.048 6454 Dihedral : 6.233 104.468 5333 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.13), residues: 4784 helix: 2.26 (0.11), residues: 2495 sheet: 0.88 (0.23), residues: 492 loop : -0.97 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.000 HIS a 146 PHE 0.023 0.001 PHE 9 74 TYR 0.020 0.001 TYR a 145 ARG 0.005 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 4.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 309 TYR cc_start: 0.8351 (t80) cc_final: 0.8106 (t80) REVERT: F 324 PHE cc_start: 0.7068 (t80) cc_final: 0.6444 (t80) REVERT: 1 75 MET cc_start: 0.7917 (ppp) cc_final: 0.7677 (ppp) REVERT: 9 48 GLU cc_start: 0.8346 (tp30) cc_final: 0.8012 (tm-30) REVERT: 9 70 ILE cc_start: 0.8502 (tp) cc_final: 0.8210 (tp) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.4461 time to fit residues: 283.6750 Evaluate side-chains 265 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 385 optimal weight: 0.0370 chunk 262 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 344 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 395 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 415 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36559 Z= 0.209 Angle : 0.533 11.679 49641 Z= 0.270 Chirality : 0.040 0.287 5826 Planarity : 0.004 0.060 6454 Dihedral : 6.083 98.760 5333 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % 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: 1.34 (0.12), residues: 4784 helix: 2.22 (0.11), residues: 2493 sheet: 0.71 (0.23), residues: 508 loop : -1.04 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 118 HIS 0.005 0.001 HIS F 117 PHE 0.030 0.001 PHE 6 80 TYR 0.010 0.001 TYR D 379 ARG 0.006 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 3.951 Fit side-chains revert: symmetry clash REVERT: G 293 ILE cc_start: 0.8350 (tt) cc_final: 0.8091 (tt) REVERT: a 188 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7816 (tpm170) REVERT: 1 75 MET cc_start: 0.7964 (ppp) cc_final: 0.7749 (ppp) REVERT: 9 48 GLU cc_start: 0.8349 (tp30) cc_final: 0.8005 (tm-30) REVERT: 9 65 GLU cc_start: 0.7163 (mp0) cc_final: 0.6510 (mp0) REVERT: 9 70 ILE cc_start: 0.8477 (tp) cc_final: 0.8127 (tp) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.4000 time to fit residues: 244.5589 Evaluate side-chains 264 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 155 optimal weight: 4.9990 chunk 416 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 463 optimal weight: 7.9990 chunk 384 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN E 68 GLN F 55 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36559 Z= 0.256 Angle : 0.575 11.448 49641 Z= 0.291 Chirality : 0.041 0.268 5826 Planarity : 0.004 0.058 6454 Dihedral : 6.063 88.978 5333 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % 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: 1.14 (0.12), residues: 4784 helix: 2.09 (0.11), residues: 2486 sheet: 0.55 (0.23), residues: 503 loop : -1.15 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 118 HIS 0.006 0.001 HIS D 117 PHE 0.024 0.001 PHE D 240 TYR 0.014 0.001 TYR 1 68 ARG 0.007 0.000 ARG D 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 347 time to evaluate : 3.827 Fit side-chains REVERT: A 229 MET cc_start: 0.8288 (tpp) cc_final: 0.8020 (tpp) REVERT: G 301 ASN cc_start: 0.8225 (t0) cc_final: 0.7976 (t0) REVERT: 1 75 MET cc_start: 0.7778 (ppp) cc_final: 0.7570 (ppp) REVERT: 3 75 MET cc_start: 0.6981 (tmm) cc_final: 0.6306 (tmm) REVERT: 5 15 ILE cc_start: 0.5634 (mm) cc_final: 0.5354 (mm) REVERT: 9 48 GLU cc_start: 0.8424 (tp30) cc_final: 0.8065 (tm-30) REVERT: 9 65 GLU cc_start: 0.7311 (mp0) cc_final: 0.6618 (mm-30) REVERT: 9 70 ILE cc_start: 0.8477 (tp) cc_final: 0.8158 (tp) outliers start: 1 outliers final: 0 residues processed: 348 average time/residue: 0.4031 time to fit residues: 244.4770 Evaluate side-chains 254 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 446 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 chunk 338 optimal weight: 0.3980 chunk 262 optimal weight: 0.9990 chunk 390 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 461 optimal weight: 2.9990 chunk 288 optimal weight: 0.4980 chunk 281 optimal weight: 0.9980 chunk 213 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN E 68 GLN F 55 GLN d 220 ASN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36559 Z= 0.145 Angle : 0.532 11.406 49641 Z= 0.264 Chirality : 0.040 0.266 5826 Planarity : 0.004 0.077 6454 Dihedral : 5.833 77.615 5333 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 1.29 (0.12), residues: 4784 helix: 2.17 (0.11), residues: 2490 sheet: 0.77 (0.23), residues: 492 loop : -1.07 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 118 HIS 0.004 0.001 HIS a 146 PHE 0.023 0.001 PHE 6 80 TYR 0.009 0.001 TYR C 400 ARG 0.004 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 3.989 Fit side-chains REVERT: B 303 TYR cc_start: 0.8669 (t80) cc_final: 0.8468 (t80) REVERT: 1 21 MET cc_start: 0.5715 (tpt) cc_final: 0.5501 (tpt) REVERT: 1 58 PHE cc_start: 0.7143 (m-10) cc_final: 0.6900 (m-10) REVERT: 1 75 MET cc_start: 0.7852 (ppp) cc_final: 0.7628 (ppp) REVERT: 3 75 MET cc_start: 0.6886 (tmm) cc_final: 0.6151 (tmm) REVERT: 5 15 ILE cc_start: 0.5619 (mm) cc_final: 0.5329 (mm) REVERT: 9 48 GLU cc_start: 0.8359 (tp30) cc_final: 0.8023 (tm-30) REVERT: 9 65 GLU cc_start: 0.6890 (mp0) cc_final: 0.6479 (mp0) REVERT: 9 70 ILE cc_start: 0.8502 (tp) cc_final: 0.8075 (tp) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.4208 time to fit residues: 261.3391 Evaluate side-chains 259 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 285 optimal weight: 0.0470 chunk 184 optimal weight: 6.9990 chunk 275 optimal weight: 0.0870 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 0.0060 chunk 89 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 overall best weight: 0.6276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36559 Z= 0.149 Angle : 0.533 11.019 49641 Z= 0.263 Chirality : 0.040 0.304 5826 Planarity : 0.004 0.059 6454 Dihedral : 5.692 70.913 5333 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 1.31 (0.12), residues: 4784 helix: 2.17 (0.11), residues: 2492 sheet: 0.82 (0.23), residues: 492 loop : -1.03 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 118 HIS 0.004 0.001 HIS a 146 PHE 0.035 0.001 PHE 5 80 TYR 0.011 0.001 TYR a 145 ARG 0.023 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 4.090 Fit side-chains REVERT: a 190 PHE cc_start: 0.8299 (t80) cc_final: 0.8083 (t80) REVERT: 1 21 MET cc_start: 0.5816 (tpt) cc_final: 0.5598 (tpt) REVERT: 1 58 PHE cc_start: 0.7076 (m-10) cc_final: 0.6806 (m-10) REVERT: 1 75 MET cc_start: 0.7817 (ppp) cc_final: 0.7564 (ppp) REVERT: 3 75 MET cc_start: 0.6873 (tmm) cc_final: 0.6187 (tmm) REVERT: 5 15 ILE cc_start: 0.5717 (mm) cc_final: 0.5438 (mm) REVERT: 9 48 GLU cc_start: 0.8364 (tp30) cc_final: 0.8028 (tm-30) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.4114 time to fit residues: 251.0021 Evaluate side-chains 259 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 419 optimal weight: 0.3980 chunk 442 optimal weight: 0.8980 chunk 403 optimal weight: 5.9990 chunk 430 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 388 optimal weight: 0.9990 chunk 406 optimal weight: 2.9990 chunk 428 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36559 Z= 0.180 Angle : 0.550 10.722 49641 Z= 0.273 Chirality : 0.040 0.289 5826 Planarity : 0.004 0.058 6454 Dihedral : 5.661 69.252 5333 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.12), residues: 4784 helix: 2.18 (0.11), residues: 2484 sheet: 0.78 (0.23), residues: 498 loop : -1.05 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 118 HIS 0.004 0.001 HIS a 146 PHE 0.028 0.001 PHE 5 80 TYR 0.012 0.001 TYR a 145 ARG 0.018 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 4.358 Fit side-chains REVERT: a 190 PHE cc_start: 0.8421 (t80) cc_final: 0.8196 (t80) REVERT: 1 58 PHE cc_start: 0.7057 (m-10) cc_final: 0.6837 (m-10) REVERT: 3 75 MET cc_start: 0.6885 (tmm) cc_final: 0.6197 (tmm) REVERT: 9 48 GLU cc_start: 0.8368 (tp30) cc_final: 0.8035 (tm-30) REVERT: 9 70 ILE cc_start: 0.8585 (tp) cc_final: 0.8254 (tp) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.4517 time to fit residues: 273.7473 Evaluate side-chains 259 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 282 optimal weight: 0.9990 chunk 454 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 316 optimal weight: 0.8980 chunk 477 optimal weight: 9.9990 chunk 439 optimal weight: 7.9990 chunk 380 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 293 optimal weight: 0.9990 chunk 233 optimal weight: 0.0270 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN D 175 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 377 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36559 Z= 0.148 Angle : 0.543 11.135 49641 Z= 0.266 Chirality : 0.040 0.238 5826 Planarity : 0.004 0.060 6454 Dihedral : 5.557 70.286 5333 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.43 % Rotamer: Outliers : 0.03 % Allowed : 0.42 % Favored : 99.55 % 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: 1.35 (0.13), residues: 4784 helix: 2.21 (0.11), residues: 2481 sheet: 0.83 (0.23), residues: 493 loop : -1.01 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 118 HIS 0.005 0.000 HIS a 146 PHE 0.026 0.001 PHE 5 80 TYR 0.015 0.001 TYR 6 68 ARG 0.012 0.000 ARG a 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 4.019 Fit side-chains REVERT: D 355 ILE cc_start: 0.8941 (tp) cc_final: 0.8601 (tp) REVERT: a 190 PHE cc_start: 0.8431 (t80) cc_final: 0.8225 (t80) REVERT: 1 58 PHE cc_start: 0.7079 (m-10) cc_final: 0.6797 (m-10) REVERT: 1 75 MET cc_start: 0.7713 (ppp) cc_final: 0.7460 (ppp) REVERT: 9 48 GLU cc_start: 0.8358 (tp30) cc_final: 0.8031 (tm-30) REVERT: 9 70 ILE cc_start: 0.8649 (tp) cc_final: 0.8293 (tp) outliers start: 1 outliers final: 1 residues processed: 354 average time/residue: 0.4100 time to fit residues: 252.6775 Evaluate side-chains 269 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 4.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 301 optimal weight: 6.9990 chunk 404 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 350 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 380 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 390 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN D 175 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN d 156 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.065712 restraints weight = 142545.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066049 restraints weight = 105942.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066051 restraints weight = 74756.701| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36559 Z= 0.161 Angle : 0.544 10.943 49641 Z= 0.268 Chirality : 0.040 0.295 5826 Planarity : 0.004 0.060 6454 Dihedral : 5.509 69.090 5333 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.82 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 1.34 (0.12), residues: 4784 helix: 2.20 (0.11), residues: 2481 sheet: 0.83 (0.23), residues: 489 loop : -1.01 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 118 HIS 0.004 0.001 HIS a 146 PHE 0.024 0.001 PHE 5 80 TYR 0.012 0.001 TYR a 145 ARG 0.010 0.000 ARG a 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6216.80 seconds wall clock time: 113 minutes 48.61 seconds (6828.61 seconds total)