Starting phenix.real_space_refine on Mon Apr 15 20:38:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5c_33616/04_2024/7y5c_33616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5c_33616/04_2024/7y5c_33616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5c_33616/04_2024/7y5c_33616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5c_33616/04_2024/7y5c_33616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5c_33616/04_2024/7y5c_33616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5c_33616/04_2024/7y5c_33616_updated.pdb" } resolution = 4.7 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 22837 2.51 5 N 6247 2.21 5 O 6781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 254": "OD1" <-> "OD2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 462": "OD1" <-> "OD2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 32": "OD1" <-> "OD2" Residue "9 GLU 65": "OE1" <-> "OE2" Residue "3 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35993 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3925 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 504} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3777 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "C" 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: "D" 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: "E" 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: "F" 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: "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: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3007 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 11, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 174 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': 12} Unresolved non-hydrogen planarities: 147 Chain: "7" 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: "8" 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: "9" 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: "1" 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: "2" 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: "3" 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: "4" 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: "5" 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: "6" 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 18.34, per 1000 atoms: 0.51 Number of scatterers: 35993 At special positions: 0 Unit cell: (174.9, 126.5, 237.6, 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 6781 8.00 N 6247 7.00 C 22837 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: 14.47 Conformation dependent library (CDL) restraints added in 6.9 seconds 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 26 sheets defined 52.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.87 Creating SS restraints... Processing helix chain 'A' and resid 6 through 21 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.888A pdb=" N CYS A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.777A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.740A 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: 4.058A pdb=" N PHE A 302 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.925A pdb=" N ILE A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 406 Processing helix chain 'A' and resid 415 through 430 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 477 removed outlier: 5.265A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 466 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 467 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 472 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 194 removed outlier: 4.542A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.502A 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 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.837A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 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 299 through 309 removed outlier: 4.081A pdb=" N PHE B 302 " --> pdb=" O GLY B 299 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 309 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 390 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 464 through 478 Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.856A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 21 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.841A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.641A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.936A 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 299 through 310 removed outlier: 4.002A pdb=" N PHE C 302 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 310 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 removed outlier: 4.025A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 430 Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 464 through 477 Processing helix chain 'C' and resid 481 through 488 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 166 through 179 removed outlier: 4.012A pdb=" N ARG D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.777A pdb=" N LYS D 211 " --> pdb=" O ASN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 Processing helix chain 'D' and resid 230 through 245 removed outlier: 3.522A pdb=" N GLU D 244 " --> pdb=" O PHE D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 283 through 293 removed outlier: 4.346A 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: 3.657A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 363 through 388 removed outlier: 4.882A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 411 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 432 through 444 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 461 through 470 Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 206 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 245 removed outlier: 5.445A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 270 removed outlier: 3.606A pdb=" N LEU E 270 " --> pdb=" O VAL E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 293 removed outlier: 4.728A 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: 3.524A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N HIS E 326 " --> pdb=" O THR E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 340 Processing helix chain 'E' and resid 363 through 388 removed outlier: 4.487A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 412 Processing helix chain 'E' and resid 418 through 421 Processing helix chain 'E' and resid 432 through 444 removed outlier: 4.159A pdb=" N LYS E 444 " --> pdb=" O ASP E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 462 through 469 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 142 through 147 Processing helix chain 'F' and resid 166 through 180 Processing helix chain 'F' and resid 194 through 207 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 245 removed outlier: 5.346A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 270 removed outlier: 3.712A pdb=" N THR F 260 " --> pdb=" O ILE F 256 " (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 284 through 292 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: 3.761A pdb=" N THR F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.331A 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 386 removed outlier: 4.269A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 411 removed outlier: 4.383A pdb=" N LEU F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 421 removed outlier: 4.607A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 469 Processing helix chain 'G' and resid 6 through 42 removed outlier: 3.690A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 removed outlier: 3.948A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.683A pdb=" N ASP G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.704A 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: 3.965A 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: 3.661A pdb=" N LEU G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU G 249 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG G 261 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 263 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 4.144A 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: 3.820A pdb=" N LEU H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 52 removed outlier: 3.854A pdb=" N ALA a 51 " --> pdb=" O PHE a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 78 Processing helix chain 'a' and resid 89 through 108 removed outlier: 4.034A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 151 removed outlier: 3.829A pdb=" N ALA a 148 " --> pdb=" O CYS a 144 " (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: 3.610A pdb=" N THR a 220 " --> pdb=" O ALA a 216 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 48 removed outlier: 3.986A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 58 removed outlier: 4.629A pdb=" N LYS b 55 " --> pdb=" O PRO b 51 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL b 56 " --> pdb=" O PRO b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 146 removed outlier: 3.773A pdb=" N SER b 74 " --> pdb=" O ASP b 70 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA b 75 " --> pdb=" O ASN b 71 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER b 134 " --> pdb=" O ASP b 130 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN b 139 " --> pdb=" O ALA b 135 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) removed outlier: 5.298A 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 4 through 17 removed outlier: 4.507A pdb=" N ILE d 9 " --> pdb=" O ILE d 5 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY d 10 " --> pdb=" O GLY d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 19 through 55 removed outlier: 3.701A pdb=" N VAL d 22 " --> pdb=" O VAL d 19 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL d 23 " --> pdb=" O LYS d 20 " (cutoff:3.500A) Proline residue: d 24 - end of helix removed outlier: 3.799A pdb=" N ASP d 55 " --> pdb=" O ALA d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 57 through 135 Processing helix chain 'd' and resid 140 through 156 removed outlier: 3.935A pdb=" N SER d 144 " --> pdb=" O PRO d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 193 removed outlier: 4.573A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY d 193 " --> pdb=" O SER d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 215 Processing helix chain 'd' and resid 217 through 223 Processing helix chain 'd' and resid 231 through 239 Processing helix chain 'd' and resid 242 through 244 No H-bonds generated for 'chain 'd' and resid 242 through 244' Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 284 removed outlier: 3.708A pdb=" N VAL d 271 " --> pdb=" O LEU d 267 " (cutoff:3.500A) removed outlier: 3.783A 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 313 Processing helix chain 'd' and resid 322 through 330 Processing helix chain 'd' and resid 339 through 351 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 '7' and resid 7 through 45 removed outlier: 3.739A pdb=" N ALA 7 44 " --> pdb=" O ILE 7 40 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG 7 45 " --> pdb=" O SER 7 41 " (cutoff:3.500A) Processing helix chain '7' and resid 50 through 52 No H-bonds generated for 'chain '7' and resid 50 through 52' Processing helix chain '7' and resid 54 through 80 removed outlier: 3.679A pdb=" N VAL 7 64 " --> pdb=" O THR 7 60 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 45 Processing helix chain '8' and resid 51 through 79 removed outlier: 4.485A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix Processing helix chain '9' and resid 6 through 45 Processing helix chain '9' and resid 54 through 79 Processing helix chain '1' and resid 6 through 45 Processing helix chain '1' and resid 55 through 78 removed outlier: 3.792A pdb=" N ALA 1 67 " --> pdb=" O LEU 1 63 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR 1 68 " --> pdb=" O VAL 1 64 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU 1 77 " --> pdb=" O ALA 1 73 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE 1 78 " --> pdb=" O PHE 1 74 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 44 removed outlier: 3.791A pdb=" N ILE 2 43 " --> pdb=" O LEU 2 39 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 55 through 80 Processing helix chain '3' and resid 7 through 45 removed outlier: 3.712A pdb=" N ARG 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 50 through 52 No H-bonds generated for 'chain '3' and resid 50 through 52' Processing helix chain '3' and resid 55 through 80 removed outlier: 3.675A pdb=" N LEU 3 63 " --> pdb=" O ILE 3 59 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL 3 64 " --> pdb=" O THR 3 60 " (cutoff:3.500A) Processing helix chain '4' and resid 7 through 45 Processing helix chain '4' and resid 55 through 80 Processing helix chain '5' and resid 5 through 44 Processing helix chain '5' and resid 50 through 52 No H-bonds generated for 'chain '5' and resid 50 through 52' Processing helix chain '5' and resid 54 through 81 removed outlier: 3.669A pdb=" N LEU 5 63 " --> pdb=" O ILE 5 59 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL 5 64 " --> pdb=" O THR 5 60 " (cutoff:3.500A) Processing helix chain '6' and resid 7 through 45 removed outlier: 3.792A pdb=" N ALA 6 11 " --> pdb=" O ILE 6 8 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 80 Processing sheet with id= A, first strand: chain 'A' and resid 33 through 38 removed outlier: 3.767A pdb=" N THR A 33 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 68 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 removed outlier: 3.688A pdb=" N THR A 128 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 352 through 354 removed outlier: 8.669A pdb=" N CYS A 353 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLN A 168 " --> pdb=" O MET A 324 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY A 326 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 170 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLY A 172 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 330 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A 267 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N LEU A 327 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A 269 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE A 329 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE A 271 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLU A 331 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 233 " --> pdb=" O CYS A 204 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.869A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 42 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 55 through 57 Processing sheet with id= F, first strand: chain 'B' and resid 99 through 102 Processing sheet with id= G, first strand: chain 'B' and resid 170 through 172 Processing sheet with id= H, first strand: chain 'B' and resid 232 through 237 removed outlier: 9.182A pdb=" N THR B 233 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS B 266 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL B 205 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 268 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 207 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 270 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE B 209 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 325 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 271 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.517A pdb=" N GLU C 57 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.562A pdb=" N VAL C 100 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 130 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 352 through 354 removed outlier: 6.944A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 168 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 207 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 233 " --> pdb=" O CYS C 204 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.646A pdb=" N VAL D 13 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 47 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 40 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 87 through 89 removed outlier: 3.512A pdb=" N TRP D 118 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 329 through 332 removed outlier: 3.609A pdb=" N ALA D 329 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA D 157 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 19 through 23 removed outlier: 3.597A pdb=" N ILE E 65 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU E 52 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS E 47 " --> pdb=" O ILE E 40 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 87 through 90 Processing sheet with id= Q, first strand: chain 'E' and resid 329 through 332 removed outlier: 3.725A pdb=" N ALA E 329 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA E 214 " --> pdb=" O SER E 185 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 19 through 23 removed outlier: 3.684A pdb=" N GLN F 55 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS F 47 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 49 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 87 through 90 Processing sheet with id= T, first strand: chain 'F' and resid 156 through 159 removed outlier: 6.958A pdb=" N ALA F 329 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N PHE F 159 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR F 331 " --> pdb=" O PHE F 159 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 249 through 252 removed outlier: 6.838A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 78 through 82 removed outlier: 6.379A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'G' and resid 184 through 190 removed outlier: 3.637A pdb=" N THR G 197 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.699A pdb=" N LEU H 4 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG H 78 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER H 71 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU H 80 " --> pdb=" O PHE H 69 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 31 through 33 removed outlier: 3.603A pdb=" N THR H 25 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA H 49 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA H 64 " --> pdb=" O GLN H 85 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN H 85 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'd' and resid 408 through 411 1937 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: 12.78 Time building geometry restraints manager: 15.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12067 1.34 - 1.46: 5398 1.46 - 1.58: 18911 1.58 - 1.70: 27 1.70 - 1.82: 192 Bond restraints: 36595 Sorted by residual: bond pdb=" N GLU A 295 " pdb=" CA GLU A 295 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.50e+00 bond pdb=" C PRO b 51 " pdb=" N PRO b 52 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.27e+00 bond pdb=" CA GLY B 363 " pdb=" C GLY B 363 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.51e+00 bond pdb=" CA PRO F 223 " pdb=" C PRO F 223 " ideal model delta sigma weight residual 1.514 1.523 -0.009 5.50e-03 3.31e+04 2.49e+00 bond pdb=" CG1 ILE 7 26 " pdb=" CD1 ILE 7 26 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.92e+00 ... (remaining 36590 not shown) Histogram of bond angle deviations from ideal: 95.71 - 104.55: 612 104.55 - 113.39: 20583 113.39 - 122.23: 23131 122.23 - 131.07: 5257 131.07 - 139.92: 104 Bond angle restraints: 49687 Sorted by residual: angle pdb=" N ILE E 458 " pdb=" CA ILE E 458 " pdb=" C ILE E 458 " ideal model delta sigma weight residual 113.71 108.35 5.36 9.50e-01 1.11e+00 3.18e+01 angle pdb=" N VAL E 209 " pdb=" CA VAL E 209 " pdb=" C VAL E 209 " ideal model delta sigma weight residual 113.20 108.53 4.67 9.60e-01 1.09e+00 2.37e+01 angle pdb=" N ILE B 337 " pdb=" CA ILE B 337 " pdb=" C ILE B 337 " ideal model delta sigma weight residual 113.53 109.64 3.89 9.80e-01 1.04e+00 1.58e+01 angle pdb=" C PHE 1 74 " pdb=" N MET 1 75 " pdb=" CA MET 1 75 " ideal model delta sigma weight residual 122.06 115.48 6.58 1.86e+00 2.89e-01 1.25e+01 angle pdb=" N ILE D 355 " pdb=" CA ILE D 355 " pdb=" C ILE D 355 " ideal model delta sigma weight residual 113.20 109.97 3.23 9.60e-01 1.09e+00 1.13e+01 ... (remaining 49682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 20720 26.14 - 52.28: 1040 52.28 - 78.42: 123 78.42 - 104.56: 18 104.56 - 130.70: 1 Dihedral angle restraints: 21902 sinusoidal: 8272 harmonic: 13630 Sorted by residual: dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 169.30 130.70 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" CA ARG A 294 " pdb=" C ARG A 294 " pdb=" N GLU A 295 " pdb=" CA GLU A 295 " ideal model delta harmonic sigma weight residual -180.00 -157.04 -22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" O2A ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PA ADP E 501 " pdb=" PB ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 -134.55 74.55 1 2.00e+01 2.50e-03 1.76e+01 ... (remaining 21899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 4201 0.039 - 0.077: 1169 0.077 - 0.116: 397 0.116 - 0.154: 57 0.154 - 0.193: 4 Chirality restraints: 5828 Sorted by residual: chirality pdb=" CA GLU A 295 " pdb=" N GLU A 295 " pdb=" C GLU A 295 " pdb=" CB GLU A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CB ILE 6 20 " pdb=" CA ILE 6 20 " pdb=" CG1 ILE 6 20 " pdb=" CG2 ILE 6 20 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA LYS a 181 " pdb=" N LYS a 181 " pdb=" C LYS a 181 " pdb=" CB LYS a 181 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 5825 not shown) Planarity restraints: 6459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 4 54 " 0.025 2.00e-02 2.50e+03 2.11e-02 7.77e+00 pdb=" CG PHE 4 54 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE 4 54 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE 4 54 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 4 54 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 4 54 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE 4 54 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 257 " -0.015 2.00e-02 2.50e+03 1.88e-02 6.20e+00 pdb=" CG PHE D 257 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE D 257 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE D 257 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 257 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 257 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 257 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 6 32 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C ASP 6 32 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP 6 32 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY 6 33 " -0.014 2.00e-02 2.50e+03 ... (remaining 6456 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 221 2.51 - 3.11: 27733 3.11 - 3.71: 57051 3.71 - 4.30: 71092 4.30 - 4.90: 117140 Nonbonded interactions: 273237 Sorted by model distance: nonbonded pdb="MG MG D 500 " pdb=" O2A ATP D 501 " model vdw 1.916 2.170 nonbonded pdb="MG MG D 500 " pdb=" O1B ATP D 501 " model vdw 1.925 2.170 nonbonded pdb="MG MG F 500 " pdb=" O3B ATP F 501 " model vdw 1.963 2.170 nonbonded pdb="MG MG A 600 " pdb=" O1G ATP A 601 " model vdw 2.005 2.170 nonbonded pdb="MG MG B 600 " pdb=" O1A ATP B 601 " model vdw 2.008 2.170 ... (remaining 273232 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 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 '2' 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 '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 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 '5' 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 '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 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 11 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 22 or resid 28 through 190 or (res \ id 191 through 192 and (name N or name CA or name C or name O or name CB )) or r \ esid 193 through 316 or (resid 317 through 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 (resid 494 through 499 and (name N or name CA or \ name C or name O or name CB )) or resid 500 through 516 or resid 537 through 53 \ 8 or resid 540 or resid 600 through 601)) selection = (chain 'B' and ((resid 11 through 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 132 or (resid 133 and (name N or name CA or na \ me C or name 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 (nam \ e N or name CA or name C or name O or name CB )) or resid 359 through 400 or (re \ sid 401 through 402 and (name N or name CA or name 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 o \ r name CB )) or resid 413 through 416 or (resid 417 through 419 and (name N or n \ ame CA or name 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 46 \ 4 through 467 or (resid 468 and (name N or name CA or name C or name O or name C \ B )) or resid 469 or (resid 470 and (name N or name CA or name C or name O or na \ me 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 600 through 601)) selection = (chain 'C' and ((resid 11 through 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 132 or (resid 133 and (name N or name CA or na \ me C or name 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 31 \ 6 or (resid 317 through 318 and (name N or name CA or name C or name O or name C \ B )) or resid 319 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 401 or (resid 402 and (name N or n \ ame CA or name 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 41 \ 6 or (resid 417 through 419 and (name N or name CA or name C or name O or name C \ B )) or resid 420 through 456 or (resid 457 and (name N or name CA or name C or \ name O or name 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 thro \ ugh 499 and (name N or name CA or name C or name O or name CB )) or resid 500 th \ rough 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 600 through 601)) } 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 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)) selection = (chain 'E' 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 'F' 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)) } 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: 6.410 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: 0.040 Extract box with map and model: 19.150 Check model and map are aligned: 0.600 Set scattering table: 0.340 Process input model: 91.120 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.190 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.003 0.054 36595 Z= 0.170 Angle : 0.596 11.386 49687 Z= 0.309 Chirality : 0.040 0.193 5828 Planarity : 0.004 0.053 6459 Dihedral : 14.530 130.699 13170 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: 1.08 (0.12), residues: 4795 helix: 1.82 (0.11), residues: 2527 sheet: 0.54 (0.24), residues: 470 loop : -0.82 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 66 HIS 0.003 0.001 HIS A 259 PHE 0.048 0.001 PHE 4 54 TYR 0.024 0.001 TYR a 240 ARG 0.011 0.000 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8691 (tpt) cc_final: 0.8407 (tpt) REVERT: B 182 CYS cc_start: 0.8998 (m) cc_final: 0.8779 (m) REVERT: C 51 MET cc_start: 0.6846 (tpp) cc_final: 0.6131 (tpp) REVERT: E 64 CYS cc_start: 0.6717 (m) cc_final: 0.6477 (m) REVERT: G 187 PHE cc_start: 0.7595 (p90) cc_final: 0.7301 (p90) REVERT: a 240 TYR cc_start: 0.7470 (m-80) cc_final: 0.7261 (m-80) REVERT: d 157 MET cc_start: 0.8699 (ppp) cc_final: 0.8201 (ppp) REVERT: 2 65 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7752 (mm-30) REVERT: 2 69 PHE cc_start: 0.8449 (m-10) cc_final: 0.8201 (m-80) REVERT: 5 75 MET cc_start: 0.5811 (mmp) cc_final: 0.5501 (tmm) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.4211 time to fit residues: 207.9330 Evaluate side-chains 203 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 4.104 ------------------------------------------------------------------------------- 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: 0.9980 chunk 363 optimal weight: 0.7980 chunk 201 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 375 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 434 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 369 ASN C 141 GLN D 55 GLN D 377 GLN E 247 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36595 Z= 0.186 Angle : 0.537 10.597 49687 Z= 0.273 Chirality : 0.040 0.157 5828 Planarity : 0.004 0.055 6459 Dihedral : 6.786 107.039 5337 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.25 % 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: 1.15 (0.12), residues: 4795 helix: 1.90 (0.10), residues: 2525 sheet: 0.58 (0.23), residues: 479 loop : -0.85 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 118 HIS 0.004 0.001 HIS B 43 PHE 0.025 0.001 PHE D 439 TYR 0.020 0.001 TYR a 240 ARG 0.005 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 CYS cc_start: 0.9007 (m) cc_final: 0.8803 (m) REVERT: B 324 MET cc_start: 0.8129 (mpp) cc_final: 0.7756 (mpp) REVERT: C 51 MET cc_start: 0.6905 (tpp) cc_final: 0.6433 (tpp) REVERT: C 149 LEU cc_start: 0.8635 (tt) cc_final: 0.8316 (tp) REVERT: F 67 MET cc_start: 0.8347 (mmp) cc_final: 0.8029 (mmm) REVERT: a 95 THR cc_start: 0.8861 (p) cc_final: 0.8489 (p) REVERT: a 233 PHE cc_start: 0.8698 (t80) cc_final: 0.8409 (t80) REVERT: d 157 MET cc_start: 0.8714 (ppp) cc_final: 0.8274 (ppp) REVERT: 1 21 MET cc_start: 0.5626 (tpt) cc_final: 0.5401 (mtt) REVERT: 2 65 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7777 (mm-30) REVERT: 2 69 PHE cc_start: 0.8473 (m-10) cc_final: 0.8215 (m-80) REVERT: 5 75 MET cc_start: 0.5916 (mmp) cc_final: 0.5568 (tmm) outliers start: 1 outliers final: 1 residues processed: 279 average time/residue: 0.4246 time to fit residues: 206.4249 Evaluate side-chains 206 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 3.958 ------------------------------------------------------------------------------- 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: 10.0000 chunk 135 optimal weight: 0.1980 chunk 362 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 435 optimal weight: 3.9990 chunk 470 optimal weight: 1.9990 chunk 388 optimal weight: 0.1980 chunk 432 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 349 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 369 ASN C 141 GLN D 55 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36595 Z= 0.148 Angle : 0.531 8.750 49687 Z= 0.265 Chirality : 0.040 0.161 5828 Planarity : 0.004 0.055 6459 Dihedral : 6.550 98.789 5337 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 1.19 (0.12), residues: 4795 helix: 1.93 (0.11), residues: 2520 sheet: 0.57 (0.24), residues: 469 loop : -0.82 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 208 HIS 0.003 0.001 HIS A 259 PHE 0.031 0.001 PHE 6 69 TYR 0.023 0.001 TYR a 240 ARG 0.004 0.000 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 MET cc_start: 0.7004 (tpp) cc_final: 0.6627 (tpp) REVERT: G 206 MET cc_start: 0.7934 (tpt) cc_final: 0.7688 (mmp) REVERT: d 11 PHE cc_start: 0.2773 (m-10) cc_final: 0.2463 (m-80) REVERT: 1 21 MET cc_start: 0.5547 (tpt) cc_final: 0.5346 (mtt) REVERT: 2 65 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7705 (mm-30) REVERT: 2 69 PHE cc_start: 0.8460 (m-10) cc_final: 0.8207 (m-80) REVERT: 5 75 MET cc_start: 0.5865 (mmp) cc_final: 0.5502 (tmm) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.4909 time to fit residues: 243.8413 Evaluate side-chains 208 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 4.388 ------------------------------------------------------------------------------- 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: 0.0870 chunk 327 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 437 optimal weight: 9.9990 chunk 463 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 414 optimal weight: 0.0060 chunk 124 optimal weight: 6.9990 overall best weight: 3.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 258 GLN B 361 ASN B 369 ASN B 512 GLN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 HIS ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN H 5 ASN H 38 HIS ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 71 ASN ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN 6 50 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 36595 Z= 0.346 Angle : 0.685 12.358 49687 Z= 0.353 Chirality : 0.044 0.185 5828 Planarity : 0.005 0.060 6459 Dihedral : 6.900 83.265 5337 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.12), residues: 4795 helix: 1.45 (0.10), residues: 2511 sheet: 0.08 (0.24), residues: 448 loop : -1.00 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 208 HIS 0.010 0.002 HIS A 266 PHE 0.035 0.002 PHE 6 69 TYR 0.026 0.002 TYR B 262 ARG 0.012 0.001 ARG D 378 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8804 (tpt) cc_final: 0.8487 (tpt) REVERT: B 324 MET cc_start: 0.8047 (mpp) cc_final: 0.7783 (mpp) REVERT: B 361 ASN cc_start: 0.9066 (t0) cc_final: 0.8633 (t0) REVERT: C 51 MET cc_start: 0.7023 (tpp) cc_final: 0.6746 (tpp) REVERT: D 379 TYR cc_start: 0.7764 (t80) cc_final: 0.7533 (t80) REVERT: F 309 TYR cc_start: 0.9053 (t80) cc_final: 0.8771 (t80) REVERT: G 206 MET cc_start: 0.8152 (tpt) cc_final: 0.7898 (mmp) REVERT: a 233 PHE cc_start: 0.8739 (t80) cc_final: 0.8274 (t80) REVERT: d 157 MET cc_start: 0.8660 (ppp) cc_final: 0.8082 (ppp) REVERT: 2 65 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7742 (mm-30) REVERT: 2 69 PHE cc_start: 0.8571 (m-10) cc_final: 0.8297 (m-80) REVERT: 3 60 THR cc_start: 0.6093 (m) cc_final: 0.5803 (p) REVERT: 5 75 MET cc_start: 0.5704 (mmp) cc_final: 0.5487 (tmm) REVERT: 6 21 MET cc_start: 0.6818 (tpp) cc_final: 0.6545 (tpp) outliers start: 2 outliers final: 1 residues processed: 266 average time/residue: 0.4408 time to fit residues: 200.7425 Evaluate side-chains 189 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 4.251 ------------------------------------------------------------------------------- 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: 0.5980 chunk 262 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 344 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 395 optimal weight: 6.9990 chunk 320 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 236 optimal weight: 0.9980 chunk 415 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN C 141 GLN C 168 GLN D 55 GLN E 421 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 71 ASN 1 71 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36595 Z= 0.153 Angle : 0.571 10.990 49687 Z= 0.284 Chirality : 0.041 0.186 5828 Planarity : 0.004 0.057 6459 Dihedral : 6.417 79.650 5337 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.12), residues: 4795 helix: 1.74 (0.10), residues: 2520 sheet: 0.30 (0.24), residues: 459 loop : -0.85 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 118 HIS 0.005 0.001 HIS D 117 PHE 0.027 0.001 PHE d 11 TYR 0.026 0.001 TYR a 240 ARG 0.011 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 4.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8637 (tpt) cc_final: 0.8431 (tpt) REVERT: B 361 ASN cc_start: 0.9236 (t0) cc_final: 0.8883 (t0) REVERT: C 51 MET cc_start: 0.7063 (tpp) cc_final: 0.6827 (tpp) REVERT: C 359 LEU cc_start: 0.8863 (mm) cc_final: 0.8629 (mm) REVERT: D 379 TYR cc_start: 0.7707 (t80) cc_final: 0.7469 (t80) REVERT: F 309 TYR cc_start: 0.9150 (t80) cc_final: 0.8905 (t80) REVERT: H 41 LEU cc_start: 0.4963 (tp) cc_final: 0.4533 (tt) REVERT: d 157 MET cc_start: 0.8742 (ppp) cc_final: 0.8174 (ppp) REVERT: 9 75 MET cc_start: 0.8231 (ttm) cc_final: 0.8027 (ttm) REVERT: 1 75 MET cc_start: 0.5828 (pmm) cc_final: 0.5564 (pmm) REVERT: 2 65 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7691 (mm-30) REVERT: 2 69 PHE cc_start: 0.8477 (m-10) cc_final: 0.8204 (m-80) REVERT: 5 75 MET cc_start: 0.5602 (mmp) cc_final: 0.5343 (tmm) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.4430 time to fit residues: 222.3199 Evaluate side-chains 198 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 3.879 ------------------------------------------------------------------------------- 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: 0.7980 chunk 416 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 463 optimal weight: 10.0000 chunk 384 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN C 141 GLN D 55 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN a 146 HIS ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 71 ASN ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36595 Z= 0.280 Angle : 0.630 12.954 49687 Z= 0.322 Chirality : 0.042 0.176 5828 Planarity : 0.005 0.075 6459 Dihedral : 6.551 80.619 5337 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.03 % Allowed : 3.01 % 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: 0.68 (0.12), residues: 4795 helix: 1.53 (0.10), residues: 2517 sheet: 0.05 (0.25), residues: 432 loop : -0.96 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 208 HIS 0.008 0.001 HIS A 266 PHE 0.025 0.002 PHE A 340 TYR 0.022 0.002 TYR a 240 ARG 0.006 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8727 (tpt) cc_final: 0.8439 (tpt) REVERT: B 361 ASN cc_start: 0.9142 (t0) cc_final: 0.8819 (t0) REVERT: C 51 MET cc_start: 0.7360 (tpp) cc_final: 0.7076 (tpp) REVERT: F 309 TYR cc_start: 0.9097 (t80) cc_final: 0.8784 (t80) REVERT: H 41 LEU cc_start: 0.5087 (tp) cc_final: 0.4762 (tt) REVERT: H 106 THR cc_start: 0.8628 (p) cc_final: 0.8394 (p) REVERT: a 233 PHE cc_start: 0.8728 (t80) cc_final: 0.8266 (t80) REVERT: d 30 MET cc_start: 0.5545 (mtp) cc_final: 0.5290 (ttt) REVERT: d 157 MET cc_start: 0.8798 (ppp) cc_final: 0.8118 (ppp) REVERT: 2 65 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7721 (mm-30) REVERT: 2 69 PHE cc_start: 0.8548 (m-10) cc_final: 0.8268 (m-80) REVERT: 6 21 MET cc_start: 0.7060 (tpp) cc_final: 0.6774 (tpp) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.4519 time to fit residues: 200.9508 Evaluate side-chains 187 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 4.144 ------------------------------------------------------------------------------- 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: 8.9990 chunk 52 optimal weight: 0.1980 chunk 264 optimal weight: 3.9990 chunk 338 optimal weight: 0.2980 chunk 262 optimal weight: 6.9990 chunk 390 optimal weight: 9.9990 chunk 258 optimal weight: 0.7980 chunk 461 optimal weight: 9.9990 chunk 288 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 GLN C 141 GLN D 55 GLN E 56 HIS E 121 HIS F 255 ASN ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 71 ASN 1 71 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36595 Z= 0.152 Angle : 0.569 9.435 49687 Z= 0.285 Chirality : 0.041 0.178 5828 Planarity : 0.004 0.058 6459 Dihedral : 6.230 77.402 5337 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.12), residues: 4795 helix: 1.75 (0.11), residues: 2516 sheet: 0.35 (0.25), residues: 430 loop : -0.89 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 118 HIS 0.008 0.001 HIS E 56 PHE 0.019 0.001 PHE D 439 TYR 0.026 0.001 TYR a 240 ARG 0.006 0.000 ARG C 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.7879 (mpp) cc_final: 0.7678 (mpp) REVERT: B 361 ASN cc_start: 0.9166 (t0) cc_final: 0.8831 (t0) REVERT: C 51 MET cc_start: 0.7424 (tpp) cc_final: 0.7129 (tpp) REVERT: C 359 LEU cc_start: 0.8862 (mm) cc_final: 0.8589 (mm) REVERT: D 310 VAL cc_start: 0.7300 (m) cc_final: 0.7025 (p) REVERT: F 220 MET cc_start: 0.8077 (mmt) cc_final: 0.7795 (mmt) REVERT: F 309 TYR cc_start: 0.9165 (t80) cc_final: 0.8944 (t80) REVERT: G 206 MET cc_start: 0.8012 (tpt) cc_final: 0.7672 (tpp) REVERT: H 41 LEU cc_start: 0.4934 (tp) cc_final: 0.4539 (tt) REVERT: d 11 PHE cc_start: 0.3468 (m-10) cc_final: 0.3145 (m-80) REVERT: d 30 MET cc_start: 0.5613 (mtp) cc_final: 0.5352 (ttt) REVERT: 8 71 ASN cc_start: 0.7450 (m-40) cc_final: 0.7227 (m-40) REVERT: 2 65 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7358 (mm-30) REVERT: 2 69 PHE cc_start: 0.8515 (m-10) cc_final: 0.8238 (m-80) REVERT: 6 21 MET cc_start: 0.7089 (tpp) cc_final: 0.6845 (tpp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.4384 time to fit residues: 212.0672 Evaluate side-chains 195 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 4.235 ------------------------------------------------------------------------------- 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: 0.0010 chunk 184 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 293 optimal weight: 0.1980 chunk 314 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 362 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 GLN C 435 GLN D 55 GLN D 383 GLN E 56 HIS F 306 GLN ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36595 Z= 0.141 Angle : 0.562 9.787 49687 Z= 0.279 Chirality : 0.040 0.179 5828 Planarity : 0.004 0.057 6459 Dihedral : 5.925 72.456 5337 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: 1.06 (0.12), residues: 4795 helix: 1.83 (0.11), residues: 2523 sheet: 0.55 (0.24), residues: 452 loop : -0.87 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 118 HIS 0.006 0.001 HIS G 65 PHE 0.045 0.001 PHE 6 69 TYR 0.026 0.001 TYR a 240 ARG 0.010 0.000 ARG F 407 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.5949 (tp30) cc_final: 0.5480 (tp30) REVERT: B 324 MET cc_start: 0.7986 (mpp) cc_final: 0.7453 (mpp) REVERT: B 361 ASN cc_start: 0.9187 (t0) cc_final: 0.8832 (t0) REVERT: C 51 MET cc_start: 0.7503 (tpp) cc_final: 0.7165 (tpp) REVERT: D 379 TYR cc_start: 0.7072 (t80) cc_final: 0.6821 (t80) REVERT: F 280 GLN cc_start: 0.8420 (mp10) cc_final: 0.8042 (mp10) REVERT: G 151 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8160 (ptm160) REVERT: G 206 MET cc_start: 0.7969 (tpt) cc_final: 0.7587 (tpp) REVERT: H 41 LEU cc_start: 0.4883 (tp) cc_final: 0.4478 (tt) REVERT: b 86 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8867 (tp30) REVERT: b 89 MET cc_start: 0.8453 (tmm) cc_final: 0.7906 (tmm) REVERT: d 11 PHE cc_start: 0.3212 (m-10) cc_final: 0.2769 (m-80) REVERT: d 127 ASN cc_start: 0.9195 (t0) cc_final: 0.8973 (m-40) REVERT: 8 71 ASN cc_start: 0.7459 (m-40) cc_final: 0.7213 (m-40) REVERT: 2 65 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7386 (mm-30) REVERT: 2 69 PHE cc_start: 0.8502 (m-10) cc_final: 0.8235 (m-80) REVERT: 5 75 MET cc_start: 0.6611 (tmm) cc_final: 0.6336 (mmm) REVERT: 6 21 MET cc_start: 0.6877 (tpp) cc_final: 0.6623 (tpp) REVERT: 6 53 LEU cc_start: 0.7560 (pp) cc_final: 0.6427 (mm) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.4334 time to fit residues: 209.7739 Evaluate side-chains 203 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 4.073 ------------------------------------------------------------------------------- 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: 8.9990 chunk 442 optimal weight: 8.9990 chunk 403 optimal weight: 8.9990 chunk 430 optimal weight: 0.2980 chunk 258 optimal weight: 0.0570 chunk 187 optimal weight: 0.5980 chunk 337 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 406 optimal weight: 0.9990 chunk 428 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS C 141 GLN D 55 GLN ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 71 ASN ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36595 Z= 0.148 Angle : 0.569 10.643 49687 Z= 0.280 Chirality : 0.040 0.180 5828 Planarity : 0.004 0.056 6459 Dihedral : 5.796 67.857 5337 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 1.08 (0.12), residues: 4795 helix: 1.83 (0.11), residues: 2531 sheet: 0.63 (0.24), residues: 453 loop : -0.88 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 118 HIS 0.005 0.001 HIS G 65 PHE 0.020 0.001 PHE 7 69 TYR 0.025 0.001 TYR a 240 ARG 0.009 0.000 ARG F 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 4.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 CYS cc_start: 0.8920 (m) cc_final: 0.8706 (m) REVERT: B 324 MET cc_start: 0.7994 (mpp) cc_final: 0.7450 (mpp) REVERT: B 361 ASN cc_start: 0.9189 (t0) cc_final: 0.8840 (t0) REVERT: C 51 MET cc_start: 0.7498 (tpp) cc_final: 0.7201 (tpp) REVERT: C 359 LEU cc_start: 0.8659 (mm) cc_final: 0.8446 (tp) REVERT: D 379 TYR cc_start: 0.7163 (t80) cc_final: 0.6833 (t80) REVERT: G 151 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8166 (ptm160) REVERT: G 206 MET cc_start: 0.7963 (tpt) cc_final: 0.7560 (tpp) REVERT: H 41 LEU cc_start: 0.4893 (tp) cc_final: 0.4426 (tt) REVERT: a 239 LEU cc_start: 0.9051 (tp) cc_final: 0.8840 (tp) REVERT: b 86 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8847 (tp30) REVERT: b 89 MET cc_start: 0.8506 (tmm) cc_final: 0.7915 (tmm) REVERT: d 11 PHE cc_start: 0.3331 (m-10) cc_final: 0.2866 (m-80) REVERT: 8 71 ASN cc_start: 0.7387 (m-40) cc_final: 0.7167 (m-40) REVERT: 9 21 MET cc_start: 0.4789 (ppp) cc_final: 0.4432 (ppp) REVERT: 2 65 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7376 (mm-30) REVERT: 2 69 PHE cc_start: 0.8502 (m-10) cc_final: 0.8229 (m-80) REVERT: 5 21 MET cc_start: 0.5566 (tpp) cc_final: 0.5288 (tpp) REVERT: 6 21 MET cc_start: 0.6878 (tpp) cc_final: 0.6661 (tpp) REVERT: 6 53 LEU cc_start: 0.7315 (pp) cc_final: 0.6432 (mm) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.4462 time to fit residues: 213.5388 Evaluate side-chains 205 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 4.244 ------------------------------------------------------------------------------- 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: 0.2980 chunk 454 optimal weight: 7.9990 chunk 277 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 477 optimal weight: 1.9990 chunk 439 optimal weight: 0.0570 chunk 380 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 293 optimal weight: 0.4980 chunk 233 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN C 141 GLN D 55 GLN ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 71 ASN ** 8 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36595 Z= 0.141 Angle : 0.565 9.755 49687 Z= 0.277 Chirality : 0.040 0.182 5828 Planarity : 0.004 0.056 6459 Dihedral : 5.635 62.083 5337 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 1.11 (0.12), residues: 4795 helix: 1.83 (0.11), residues: 2534 sheet: 0.70 (0.24), residues: 453 loop : -0.83 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 118 HIS 0.008 0.001 HIS G 65 PHE 0.015 0.001 PHE a 241 TYR 0.041 0.001 TYR B 262 ARG 0.008 0.000 ARG b 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.5791 (tp30) cc_final: 0.5308 (tp30) REVERT: B 182 CYS cc_start: 0.8914 (m) cc_final: 0.8708 (m) REVERT: B 324 MET cc_start: 0.7964 (mpp) cc_final: 0.7255 (mpp) REVERT: B 361 ASN cc_start: 0.9178 (t0) cc_final: 0.8832 (t0) REVERT: B 436 TYR cc_start: 0.6821 (m-80) cc_final: 0.6543 (m-80) REVERT: C 51 MET cc_start: 0.7529 (tpp) cc_final: 0.7229 (tpp) REVERT: D 379 TYR cc_start: 0.7107 (t80) cc_final: 0.6832 (t80) REVERT: F 280 GLN cc_start: 0.8398 (mp10) cc_final: 0.8154 (mp10) REVERT: G 151 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8174 (ptm160) REVERT: G 206 MET cc_start: 0.7947 (tpt) cc_final: 0.7531 (tpp) REVERT: H 41 LEU cc_start: 0.4844 (tp) cc_final: 0.4367 (tt) REVERT: b 86 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8849 (tp30) REVERT: b 89 MET cc_start: 0.8503 (tmm) cc_final: 0.7884 (tmm) REVERT: d 11 PHE cc_start: 0.3299 (m-10) cc_final: 0.2881 (m-80) REVERT: d 127 ASN cc_start: 0.9171 (t0) cc_final: 0.8941 (m-40) REVERT: 9 21 MET cc_start: 0.4802 (ppp) cc_final: 0.4268 (ppp) REVERT: 1 75 MET cc_start: 0.6019 (pmm) cc_final: 0.5768 (pmm) REVERT: 2 65 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7337 (mm-30) REVERT: 2 69 PHE cc_start: 0.8516 (m-10) cc_final: 0.8243 (m-80) REVERT: 3 75 MET cc_start: 0.6137 (tmm) cc_final: 0.5807 (tmm) REVERT: 6 53 LEU cc_start: 0.7305 (pp) cc_final: 0.6411 (mm) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.4428 time to fit residues: 211.4618 Evaluate side-chains 203 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 4.413 ------------------------------------------------------------------------------- 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: 0.9980 chunk 404 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 350 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 380 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 390 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN C 141 GLN D 55 GLN ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 71 ASN 8 71 ASN 1 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.055109 restraints weight = 291847.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.054430 restraints weight = 306515.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.054503 restraints weight = 257619.586| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36595 Z= 0.191 Angle : 0.582 9.434 49687 Z= 0.292 Chirality : 0.041 0.176 5828 Planarity : 0.004 0.057 6459 Dihedral : 5.770 59.593 5337 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 1.04 (0.12), residues: 4795 helix: 1.78 (0.11), residues: 2533 sheet: 0.44 (0.24), residues: 469 loop : -0.82 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 118 HIS 0.010 0.001 HIS G 65 PHE 0.052 0.001 PHE 6 69 TYR 0.027 0.001 TYR B 262 ARG 0.007 0.000 ARG F 407 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5857.73 seconds wall clock time: 109 minutes 15.32 seconds (6555.32 seconds total)