Starting phenix.real_space_refine on Sun Mar 24 18:03:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crc_30450/03_2024/7crc_30450_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crc_30450/03_2024/7crc_30450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crc_30450/03_2024/7crc_30450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crc_30450/03_2024/7crc_30450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crc_30450/03_2024/7crc_30450_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crc_30450/03_2024/7crc_30450_updated.pdb" } resolution = 3.02 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 248 5.16 5 C 27437 2.51 5 N 7397 2.21 5 O 8072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A GLU 928": "OE1" <-> "OE2" Residue "A ARG 937": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B ARG 657": "NH1" <-> "NH2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B ARG 937": "NH1" <-> "NH2" Residue "B ARG 1131": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 601": "NH1" <-> "NH2" Residue "C ARG 657": "NH1" <-> "NH2" Residue "C PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 693": "OE1" <-> "OE2" Residue "C GLU 714": "OE1" <-> "OE2" Residue "C ARG 937": "NH1" <-> "NH2" Residue "C ARG 1131": "NH1" <-> "NH2" Residue "C GLU 1167": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "H GLU 249": "OE1" <-> "OE2" Residue "H GLU 305": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "F GLU 249": "OE1" <-> "OE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 249": "OE1" <-> "OE2" Residue "G GLU 305": "OE1" <-> "OE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D GLU 621": "OE1" <-> "OE2" Residue "D ARG 657": "NH1" <-> "NH2" Residue "D GLU 680": "OE1" <-> "OE2" Residue "D ARG 937": "NH1" <-> "NH2" Residue "D GLU 969": "OE1" <-> "OE2" Residue "D GLU 988": "OE1" <-> "OE2" Residue "D ARG 1131": "NH1" <-> "NH2" Residue "D GLU 1182": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43168 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8850 Classifications: {'peptide': 1108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 41, 'TRANS': 1066} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 8886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8886 Classifications: {'peptide': 1112} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 41, 'TRANS': 1070} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 8844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8844 Classifications: {'peptide': 1108} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 41, 'TRANS': 1066} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1911 Chain: "H" Number of atoms: 1883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1911 Chain: "F" Number of atoms: 1883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1911 Chain: "G" Number of atoms: 1883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 237, 1875 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1911 Chain: "D" Number of atoms: 8886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8886 Classifications: {'peptide': 1112} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 41, 'TRANS': 1070} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.32, per 1000 atoms: 0.59 Number of scatterers: 43168 At special positions: 0 Unit cell: (216.286, 218.482, 141.629, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 248 16.00 P 14 15.00 O 8072 8.00 N 7397 7.00 C 27437 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: 15.80 Conformation dependent library (CDL) restraints added in 9.7 seconds 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 213 helices and 27 sheets defined 36.7% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.17 Creating SS restraints... Processing helix chain 'A' and resid 93 through 96 No H-bonds generated for 'chain 'A' and resid 93 through 96' Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 232 through 249 removed outlier: 3.807A pdb=" N SER A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.701A pdb=" N GLN A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 272 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 293 through 307 removed outlier: 5.590A pdb=" N ASP A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 356 through 363 removed outlier: 5.805A pdb=" N ASP A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 472 through 484 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 488 through 499 removed outlier: 3.842A pdb=" N ILE A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 514 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 534 through 544 Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.861A pdb=" N ARG A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 644 through 651 Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.848A pdb=" N GLU A 743 " --> pdb=" O SER A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 837 Processing helix chain 'A' and resid 857 through 861 removed outlier: 4.067A pdb=" N GLY A 860 " --> pdb=" O SER A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 885 removed outlier: 3.912A pdb=" N GLY A 884 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 952 Processing helix chain 'A' and resid 965 through 967 No H-bonds generated for 'chain 'A' and resid 965 through 967' Processing helix chain 'A' and resid 971 through 976 removed outlier: 4.169A pdb=" N ASP A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A 976 " --> pdb=" O HIS A 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 976' Processing helix chain 'A' and resid 991 through 994 Processing helix chain 'A' and resid 1055 through 1063 Processing helix chain 'B' and resid 93 through 96 No H-bonds generated for 'chain 'B' and resid 93 through 96' Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.518A pdb=" N LYS B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.649A pdb=" N GLN B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 307 removed outlier: 5.360A pdb=" N ASP B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 No H-bonds generated for 'chain 'B' and resid 317 through 320' Processing helix chain 'B' and resid 328 through 343 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 376 through 382 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'B' and resid 457 through 466 Processing helix chain 'B' and resid 472 through 484 Proline residue: B 480 - end of helix Processing helix chain 'B' and resid 488 through 499 removed outlier: 3.640A pdb=" N ILE B 493 " --> pdb=" O LYS B 489 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 514 Processing helix chain 'B' and resid 521 through 527 Processing helix chain 'B' and resid 534 through 543 Processing helix chain 'B' and resid 558 through 570 removed outlier: 4.224A pdb=" N ARG B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 594 Processing helix chain 'B' and resid 621 through 625 removed outlier: 3.504A pdb=" N GLU B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 625' Processing helix chain 'B' and resid 644 through 650 Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 833 through 837 Processing helix chain 'B' and resid 857 through 861 removed outlier: 4.078A pdb=" N GLY B 860 " --> pdb=" O SER B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 885 removed outlier: 3.785A pdb=" N GLY B 884 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 952 Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 971 through 974 No H-bonds generated for 'chain 'B' and resid 971 through 974' Processing helix chain 'B' and resid 991 through 994 Processing helix chain 'B' and resid 1055 through 1062 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 153 through 168 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 205 through 220 Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 262 through 273 removed outlier: 3.702A pdb=" N GLN C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU C 272 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 293 through 307 removed outlier: 5.630A pdb=" N ASP C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ARG C 307 " --> pdb=" O GLN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 344 Processing helix chain 'C' and resid 356 through 363 removed outlier: 5.802A pdb=" N ASP C 363 " --> pdb=" O GLU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 382 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 457 through 467 Processing helix chain 'C' and resid 472 through 484 Proline residue: C 480 - end of helix Processing helix chain 'C' and resid 488 through 500 removed outlier: 3.755A pdb=" N ILE C 493 " --> pdb=" O LYS C 489 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 500 " --> pdb=" O PHE C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 514 Processing helix chain 'C' and resid 521 through 532 removed outlier: 5.601A pdb=" N LYS C 530 " --> pdb=" O GLY C 526 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 544 Processing helix chain 'C' and resid 558 through 567 Processing helix chain 'C' and resid 590 through 593 No H-bonds generated for 'chain 'C' and resid 590 through 593' Processing helix chain 'C' and resid 622 through 625 Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 740 through 744 removed outlier: 3.833A pdb=" N GLU C 743 " --> pdb=" O SER C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 837 Processing helix chain 'C' and resid 857 through 861 removed outlier: 4.339A pdb=" N GLY C 860 " --> pdb=" O SER C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 885 removed outlier: 3.912A pdb=" N GLY C 884 " --> pdb=" O SER C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 952 Processing helix chain 'C' and resid 965 through 967 No H-bonds generated for 'chain 'C' and resid 965 through 967' Processing helix chain 'C' and resid 971 through 976 removed outlier: 4.118A pdb=" N ASP C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 976 " --> pdb=" O HIS C 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 971 through 976' Processing helix chain 'C' and resid 991 through 994 Processing helix chain 'C' and resid 1055 through 1063 Processing helix chain 'E' and resid 69 through 83 Processing helix chain 'E' and resid 87 through 101 removed outlier: 5.084A pdb=" N VAL E 95 " --> pdb=" O MET E 91 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG E 96 " --> pdb=" O LYS E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 117 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 140 through 148 removed outlier: 4.023A pdb=" N ARG E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 176 Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 199 through 209 removed outlier: 4.475A pdb=" N PHE E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 222 Processing helix chain 'E' and resid 227 through 239 removed outlier: 3.672A pdb=" N GLU E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 262 removed outlier: 3.904A pdb=" N PHE E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS E 258 " --> pdb=" O TRP E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 277 Processing helix chain 'E' and resid 296 through 309 removed outlier: 4.041A pdb=" N ARG E 308 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 Processing helix chain 'H' and resid 87 through 101 removed outlier: 4.573A pdb=" N VAL H 95 " --> pdb=" O MET H 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG H 96 " --> pdb=" O LYS H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 117 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 140 through 148 Processing helix chain 'H' and resid 158 through 176 Processing helix chain 'H' and resid 181 through 188 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 199 through 209 removed outlier: 4.341A pdb=" N PHE H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 222 Processing helix chain 'H' and resid 227 through 239 removed outlier: 3.682A pdb=" N GLU H 239 " --> pdb=" O LEU H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 261 Processing helix chain 'H' and resid 266 through 276 removed outlier: 3.926A pdb=" N TYR H 276 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 309 removed outlier: 4.058A pdb=" N ARG H 308 " --> pdb=" O GLU H 304 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE H 309 " --> pdb=" O GLU H 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 83 Processing helix chain 'F' and resid 87 through 101 removed outlier: 4.586A pdb=" N VAL F 95 " --> pdb=" O MET F 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 117 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'F' and resid 158 through 176 Processing helix chain 'F' and resid 181 through 188 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 199 through 209 removed outlier: 4.345A pdb=" N PHE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 222 Processing helix chain 'F' and resid 227 through 239 removed outlier: 3.659A pdb=" N GLU F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 262 removed outlier: 3.562A pdb=" N LYS F 262 " --> pdb=" O CYS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 276 removed outlier: 4.194A pdb=" N TYR F 276 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 309 removed outlier: 4.062A pdb=" N ARG F 308 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 83 Processing helix chain 'G' and resid 87 through 101 removed outlier: 4.906A pdb=" N VAL G 95 " --> pdb=" O MET G 91 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 117 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 140 through 148 removed outlier: 3.637A pdb=" N ARG G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 176 Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 199 through 209 removed outlier: 4.403A pdb=" N PHE G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 227 through 239 removed outlier: 3.765A pdb=" N GLU G 239 " --> pdb=" O LEU G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 262 removed outlier: 3.872A pdb=" N PHE G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS G 258 " --> pdb=" O TRP G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 277 removed outlier: 3.903A pdb=" N TYR G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 4.120A pdb=" N ARG G 308 " --> pdb=" O GLU G 304 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE G 309 " --> pdb=" O GLU G 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 No H-bonds generated for 'chain 'D' and resid 93 through 96' Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 127 through 136 removed outlier: 3.637A pdb=" N LYS D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 153 through 169 Processing helix chain 'D' and resid 182 through 187 removed outlier: 3.599A pdb=" N LYS D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 199 Processing helix chain 'D' and resid 205 through 220 removed outlier: 3.917A pdb=" N THR D 220 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 262 through 273 removed outlier: 3.521A pdb=" N GLN D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 307 removed outlier: 5.389A pdb=" N ASP D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG D 307 " --> pdb=" O GLN D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 320 No H-bonds generated for 'chain 'D' and resid 317 through 320' Processing helix chain 'D' and resid 328 through 343 removed outlier: 3.510A pdb=" N MET D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 360 Processing helix chain 'D' and resid 376 through 382 removed outlier: 3.516A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 402 through 407 Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 443 through 453 removed outlier: 3.602A pdb=" N LEU D 452 " --> pdb=" O GLU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 467 removed outlier: 3.734A pdb=" N LEU D 467 " --> pdb=" O LEU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Proline residue: D 480 - end of helix Processing helix chain 'D' and resid 488 through 499 removed outlier: 3.767A pdb=" N ILE D 493 " --> pdb=" O LYS D 489 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 521 through 527 Processing helix chain 'D' and resid 534 through 543 Processing helix chain 'D' and resid 558 through 570 removed outlier: 3.540A pdb=" N GLY D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG D 569 " --> pdb=" O ARG D 565 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 625 Processing helix chain 'D' and resid 644 through 650 Processing helix chain 'D' and resid 740 through 744 removed outlier: 3.722A pdb=" N GLU D 743 " --> pdb=" O SER D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 837 Processing helix chain 'D' and resid 857 through 861 removed outlier: 4.129A pdb=" N GLY D 860 " --> pdb=" O SER D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 885 removed outlier: 3.758A pdb=" N GLY D 884 " --> pdb=" O SER D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 952 removed outlier: 3.990A pdb=" N MET D 951 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 971 through 974 No H-bonds generated for 'chain 'D' and resid 971 through 974' Processing helix chain 'D' and resid 1055 through 1063 Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.206A pdb=" N ILE A 172 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL A 143 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET A 174 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU A 145 " --> pdb=" O MET A 174 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 176 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 413 through 415 removed outlier: 8.327A pdb=" N TYR A 414 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY A 284 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 283 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 395 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 285 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 397 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 366 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 396 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 368 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR A 398 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 370 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 310 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N VAL A 369 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 312 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP A 371 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET A 314 " --> pdb=" O ASP A 371 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 819 through 821 removed outlier: 3.569A pdb=" N ASN A 821 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLN A 581 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 606 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 583 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU A 608 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 843 through 845 removed outlier: 6.183A pdb=" N VAL A 867 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 891 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU A 870 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A 893 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 914 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N MET A 894 " --> pdb=" O THR A 914 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASN A 916 " --> pdb=" O MET A 894 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR A 935 " --> pdb=" O LEU A 915 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 917 " --> pdb=" O TYR A 935 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ARG A 937 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS A 958 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU A 938 " --> pdb=" O HIS A 958 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLN A 960 " --> pdb=" O LEU A 938 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU A 979 " --> pdb=" O ILE A 961 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 1022 through 1024 removed outlier: 6.251A pdb=" N ARG A1044 " --> pdb=" O LEU A1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 1070 through 1072 Processing sheet with id= G, first strand: chain 'A' and resid 1145 through 1148 Processing sheet with id= H, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.619A pdb=" N ILE B 140 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER B 90 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 142 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 172 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL B 143 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N MET B 174 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU B 145 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 176 " --> pdb=" O LEU B 145 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 413 through 415 removed outlier: 8.068A pdb=" N TYR B 414 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY B 284 " --> pdb=" O TYR B 414 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 395 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE B 285 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 397 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 310 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL B 369 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 312 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASP B 371 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET B 314 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 819 through 821 removed outlier: 3.736A pdb=" N ASN B 821 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 774 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLN B 581 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 606 " --> pdb=" O GLN B 581 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 583 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 608 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY B 585 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 843 through 845 removed outlier: 6.146A pdb=" N VAL B 867 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 891 " --> pdb=" O PHE B 868 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU B 870 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 893 " --> pdb=" O LEU B 870 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 914 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N MET B 894 " --> pdb=" O THR B 914 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASN B 916 " --> pdb=" O MET B 894 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR B 935 " --> pdb=" O LEU B 915 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU B 917 " --> pdb=" O TYR B 935 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG B 937 " --> pdb=" O LEU B 917 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS B 958 " --> pdb=" O LEU B 936 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU B 938 " --> pdb=" O HIS B 958 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN B 960 " --> pdb=" O LEU B 938 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU B 979 " --> pdb=" O ILE B 961 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 1070 through 1073 Processing sheet with id= M, first strand: chain 'B' and resid 1093 through 1095 Processing sheet with id= N, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.258A pdb=" N ILE C 172 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL C 143 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET C 174 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C 145 " --> pdb=" O MET C 174 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 176 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 413 through 415 removed outlier: 8.360A pdb=" N TYR C 414 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY C 284 " --> pdb=" O TYR C 414 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE C 395 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE C 285 " --> pdb=" O ILE C 395 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 397 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU C 310 " --> pdb=" O PHE C 367 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL C 369 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA C 312 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASP C 371 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET C 314 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL C 373 " --> pdb=" O MET C 314 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 819 through 821 removed outlier: 3.588A pdb=" N ASN C 821 " --> pdb=" O LEU C 797 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N GLN C 581 " --> pdb=" O ILE C 604 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 606 " --> pdb=" O GLN C 581 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 583 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU C 608 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 843 through 845 removed outlier: 6.112A pdb=" N VAL C 867 " --> pdb=" O LEU C 844 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU C 891 " --> pdb=" O PHE C 868 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU C 870 " --> pdb=" O LEU C 891 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU C 893 " --> pdb=" O LEU C 870 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR C 914 " --> pdb=" O LEU C 892 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET C 894 " --> pdb=" O THR C 914 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN C 916 " --> pdb=" O MET C 894 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR C 935 " --> pdb=" O LEU C 915 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 917 " --> pdb=" O TYR C 935 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ARG C 937 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS C 958 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU C 938 " --> pdb=" O HIS C 958 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLN C 960 " --> pdb=" O LEU C 938 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU C 979 " --> pdb=" O ILE C 961 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 1001 through 1003 removed outlier: 6.398A pdb=" N TYR C1022 " --> pdb=" O LEU C1002 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG C1044 " --> pdb=" O LEU C1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 1070 through 1073 Processing sheet with id= T, first strand: chain 'C' and resid 1093 through 1095 removed outlier: 3.657A pdb=" N LEU C1173 " --> pdb=" O LEU C1095 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 87 through 90 removed outlier: 6.591A pdb=" N ILE D 140 " --> pdb=" O PHE D 88 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER D 90 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE D 142 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE D 172 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL D 143 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET D 174 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU D 145 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE D 176 " --> pdb=" O LEU D 145 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 413 through 415 removed outlier: 8.087A pdb=" N TYR D 414 " --> pdb=" O MET D 282 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY D 284 " --> pdb=" O TYR D 414 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE D 395 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE D 285 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE D 397 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 310 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL D 369 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA D 312 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 819 through 821 removed outlier: 3.698A pdb=" N ASN D 821 " --> pdb=" O LEU D 797 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 774 " --> pdb=" O GLU D 796 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLN D 581 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE D 606 " --> pdb=" O GLN D 581 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU D 583 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU D 608 " --> pdb=" O LEU D 583 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY D 585 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 843 through 845 removed outlier: 6.139A pdb=" N VAL D 867 " --> pdb=" O LEU D 844 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU D 891 " --> pdb=" O PHE D 868 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU D 870 " --> pdb=" O LEU D 891 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU D 893 " --> pdb=" O LEU D 870 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR D 914 " --> pdb=" O LEU D 892 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N MET D 894 " --> pdb=" O THR D 914 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASN D 916 " --> pdb=" O MET D 894 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR D 935 " --> pdb=" O LEU D 915 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU D 917 " --> pdb=" O TYR D 935 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG D 937 " --> pdb=" O LEU D 917 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N HIS D 958 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU D 938 " --> pdb=" O HIS D 958 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLN D 960 " --> pdb=" O LEU D 938 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU D 979 " --> pdb=" O ILE D 961 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'D' and resid 1022 through 1024 removed outlier: 6.006A pdb=" N ARG D1044 " --> pdb=" O LEU D1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 3.571A pdb=" N ALA D1085 " --> pdb=" O CYS D1190 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS D1083 " --> pdb=" O ILE D1192 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 1093 through 1096 removed outlier: 3.621A pdb=" N LEU D1173 " --> pdb=" O LEU D1095 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER D1125 " --> pdb=" O VAL D1180 " (cutoff:3.500A) 1317 hydrogen bonds defined for protein. 3755 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: 17.94 Time building geometry restraints manager: 17.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7155 1.32 - 1.44: 11310 1.44 - 1.56: 25181 1.56 - 1.69: 22 1.69 - 1.81: 364 Bond restraints: 44032 Sorted by residual: bond pdb=" C4 ATP B1302 " pdb=" C5 ATP B1302 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 bond pdb=" C4 ATP D1302 " pdb=" C5 ATP D1302 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.21e+01 bond pdb=" C5 ATP D1302 " pdb=" C6 ATP D1302 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.90e+01 bond pdb=" C5 ATP B1302 " pdb=" C6 ATP B1302 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C8 ATP D1302 " pdb=" N7 ATP D1302 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.20e+01 ... (remaining 44027 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.39: 767 105.39 - 113.03: 24445 113.03 - 120.67: 19866 120.67 - 128.32: 14128 128.32 - 135.96: 331 Bond angle restraints: 59537 Sorted by residual: angle pdb=" PB ATP D1302 " pdb=" O3B ATP D1302 " pdb=" PG ATP D1302 " ideal model delta sigma weight residual 139.87 122.40 17.47 1.00e+00 1.00e+00 3.05e+02 angle pdb=" PB ATP B1302 " pdb=" O3B ATP B1302 " pdb=" PG ATP B1302 " ideal model delta sigma weight residual 139.87 122.63 17.24 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PA ATP D1302 " pdb=" O3A ATP D1302 " pdb=" PB ATP D1302 " ideal model delta sigma weight residual 136.83 121.54 15.29 1.00e+00 1.00e+00 2.34e+02 angle pdb=" PA ATP B1302 " pdb=" O3A ATP B1302 " pdb=" PB ATP B1302 " ideal model delta sigma weight residual 136.83 121.61 15.22 1.00e+00 1.00e+00 2.32e+02 angle pdb=" N ASP B1026 " pdb=" CA ASP B1026 " pdb=" C ASP B1026 " ideal model delta sigma weight residual 111.07 120.16 -9.09 1.07e+00 8.73e-01 7.22e+01 ... (remaining 59532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.19: 25116 20.19 - 40.37: 1511 40.37 - 60.56: 169 60.56 - 80.74: 39 80.74 - 100.93: 16 Dihedral angle restraints: 26851 sinusoidal: 11023 harmonic: 15828 Sorted by residual: dihedral pdb=" C ASP C 278 " pdb=" N ASP C 278 " pdb=" CA ASP C 278 " pdb=" CB ASP C 278 " ideal model delta harmonic sigma weight residual -122.60 -136.86 14.26 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" O1B ADP C1301 " pdb=" O3A ADP C1301 " pdb=" PB ADP C1301 " pdb=" PA ADP C1301 " ideal model delta sinusoidal sigma weight residual -60.00 40.93 -100.93 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" CA LEU B 923 " pdb=" C LEU B 923 " pdb=" N LYS B 924 " pdb=" CA LYS B 924 " ideal model delta harmonic sigma weight residual 180.00 153.42 26.58 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 26848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 6187 0.089 - 0.178: 499 0.178 - 0.267: 55 0.267 - 0.356: 10 0.356 - 0.446: 3 Chirality restraints: 6754 Sorted by residual: chirality pdb=" CA ASP C 278 " pdb=" N ASP C 278 " pdb=" C ASP C 278 " pdb=" CB ASP C 278 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA LEU D 753 " pdb=" N LEU D 753 " pdb=" C LEU D 753 " pdb=" CB LEU D 753 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CA LEU D1034 " pdb=" N LEU D1034 " pdb=" C LEU D1034 " pdb=" CB LEU D1034 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 6751 not shown) Planarity restraints: 7543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B1033 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C ARG B1033 " -0.068 2.00e-02 2.50e+03 pdb=" O ARG B1033 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU B1034 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B1034 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C LEU B1034 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU B1034 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP B1035 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 138 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C TYR H 138 " -0.055 2.00e-02 2.50e+03 pdb=" O TYR H 138 " 0.020 2.00e-02 2.50e+03 pdb=" N SER H 139 " 0.019 2.00e-02 2.50e+03 ... (remaining 7540 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1877 2.71 - 3.26: 45318 3.26 - 3.81: 69385 3.81 - 4.35: 87748 4.35 - 4.90: 143886 Nonbonded interactions: 348214 Sorted by model distance: nonbonded pdb=" OG1 THR C1155 " pdb=" OE1 GLU C1156 " model vdw 2.167 2.440 nonbonded pdb=" O SER D 949 " pdb=" OG SER D 952 " model vdw 2.198 2.440 nonbonded pdb=" O ASP A 217 " pdb=" OG1 THR A 220 " model vdw 2.213 2.440 nonbonded pdb=" O LEU C1060 " pdb=" OG1 THR C1064 " model vdw 2.217 2.440 nonbonded pdb=" O LEU A1060 " pdb=" OG1 THR A1064 " model vdw 2.219 2.440 ... (remaining 348209 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 85 through 386 or (resid 387 and (name N or name CA or nam \ e C or name O or name CB )) or resid 388 through 598 or (resid 599 and (name N o \ r name CA or name C or name O or name CB )) or resid 600 through 1195 or resid 1 \ 301)) selection = (chain 'B' and (resid 85 through 386 or (resid 387 and (name N or name CA or nam \ e C or name O or name CB )) or resid 388 through 1038 or (resid 1039 through 104 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 1043 through \ 1195 or resid 1301)) selection = (chain 'C' and (resid 85 through 598 or (resid 599 and (name N or name CA or nam \ e C or name O or name CB )) or resid 600 through 1195 or resid 1301)) selection = (chain 'D' and (resid 85 through 386 or (resid 387 and (name N or name CA or nam \ e C or name O or name CB )) or resid 388 through 1038 or (resid 1039 through 104 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 1043 through \ 1195 or resid 1301)) } ncs_group { reference = (chain 'E' and (resid 67 through 78 or resid 80 through 311)) selection = (chain 'F' and (resid 67 through 78 or resid 80 through 311)) selection = (chain 'G' and (resid 67 through 78 or resid 80 through 311)) selection = (chain 'H' and (resid 67 through 78 or resid 80 through 311)) } 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 12.340 Check model and map are aligned: 0.690 Set scattering table: 0.400 Process input model: 119.270 Find NCS groups from input model: 3.710 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 44032 Z= 0.392 Angle : 0.842 17.473 59537 Z= 0.526 Chirality : 0.052 0.446 6754 Planarity : 0.004 0.069 7543 Dihedral : 13.010 100.931 16563 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.44 % Favored : 91.34 % Rotamer: Outliers : 1.04 % Allowed : 0.69 % Favored : 98.27 % Cbeta Deviations : 0.04 % 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: -1.56 (0.12), residues: 5360 helix: 0.46 (0.12), residues: 2142 sheet: -1.70 (0.18), residues: 842 loop : -2.19 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 286 HIS 0.013 0.001 HIS C 439 PHE 0.023 0.001 PHE C 531 TYR 0.017 0.002 TYR C 935 ARG 0.012 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 342 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 ARG cc_start: 0.8022 (tpt90) cc_final: 0.7743 (tpt90) REVERT: A 1052 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8366 (mtpt) REVERT: B 422 ASP cc_start: 0.8456 (t70) cc_final: 0.8146 (t0) REVERT: B 622 LYS cc_start: 0.9588 (mmpt) cc_final: 0.9385 (mmmt) REVERT: B 984 LYS cc_start: 0.8852 (mmpt) cc_final: 0.8276 (mmmt) REVERT: B 1030 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8875 (p) REVERT: B 1124 MET cc_start: 0.8531 (ttp) cc_final: 0.8325 (ttp) REVERT: C 282 MET cc_start: 0.8239 (mtt) cc_final: 0.7743 (mtt) REVERT: C 984 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8661 (mmmt) REVERT: C 1029 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8092 (mmtm) REVERT: C 1052 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8724 (mtpt) REVERT: E 139 SER cc_start: 0.8154 (m) cc_final: 0.7922 (t) REVERT: H 301 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8856 (tm-30) REVERT: F 301 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8882 (tm-30) REVERT: G 255 MET cc_start: 0.9005 (tpp) cc_final: 0.8536 (tpt) REVERT: D 192 PHE cc_start: 0.9105 (t80) cc_final: 0.8872 (t80) REVERT: D 343 MET cc_start: 0.9276 (ttm) cc_final: 0.9000 (tpp) REVERT: D 1005 ASN cc_start: 0.8164 (m-40) cc_final: 0.7793 (p0) outliers start: 44 outliers final: 12 residues processed: 374 average time/residue: 0.5328 time to fit residues: 334.7202 Evaluate side-chains 268 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 254 time to evaluate : 5.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1029 LYS Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 990 PRO Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 994 LYS Chi-restraints excluded: chain D residue 1030 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 450 optimal weight: 5.9990 chunk 404 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 273 optimal weight: 0.0980 chunk 216 optimal weight: 0.9980 chunk 418 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 254 optimal weight: 0.6980 chunk 311 optimal weight: 1.9990 chunk 484 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 580 HIS A 618 ASN A1006 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 ASN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 GLN G 298 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 801 ASN ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44032 Z= 0.163 Angle : 0.597 9.657 59537 Z= 0.302 Chirality : 0.042 0.160 6754 Planarity : 0.003 0.052 7543 Dihedral : 6.842 109.287 5950 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.36 % Favored : 92.42 % Rotamer: Outliers : 0.71 % Allowed : 6.31 % Favored : 92.98 % 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: -1.17 (0.12), residues: 5360 helix: 0.94 (0.12), residues: 2134 sheet: -1.61 (0.18), residues: 834 loop : -2.10 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 992 HIS 0.010 0.001 HIS A 439 PHE 0.017 0.001 PHE D 677 TYR 0.020 0.001 TYR B1119 ARG 0.006 0.000 ARG H 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 302 time to evaluate : 4.768 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: A 601 ARG cc_start: 0.7909 (tpt90) cc_final: 0.7546 (tpt90) REVERT: A 976 ILE cc_start: 0.8812 (mp) cc_final: 0.8585 (tp) REVERT: A 1052 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8319 (mtpt) REVERT: B 422 ASP cc_start: 0.8404 (t70) cc_final: 0.8002 (t0) REVERT: B 622 LYS cc_start: 0.9592 (mmpt) cc_final: 0.9387 (mmmt) REVERT: B 984 LYS cc_start: 0.8922 (mmpt) cc_final: 0.8680 (mmmt) REVERT: B 1005 ASN cc_start: 0.8272 (t0) cc_final: 0.8067 (p0) REVERT: B 1124 MET cc_start: 0.8411 (ttp) cc_final: 0.8207 (ttp) REVERT: C 818 TRP cc_start: 0.8123 (t60) cc_final: 0.7886 (t60) REVERT: C 984 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8613 (mmtm) REVERT: C 1009 ASN cc_start: 0.7827 (t0) cc_final: 0.7371 (t0) REVERT: C 1052 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8587 (mtpt) REVERT: H 301 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8845 (tm-30) REVERT: F 301 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8865 (tm-30) REVERT: G 219 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9305 (tp) REVERT: G 255 MET cc_start: 0.8891 (tpp) cc_final: 0.8632 (tpt) REVERT: D 601 ARG cc_start: 0.8697 (mmp80) cc_final: 0.8412 (mmp80) REVERT: D 1005 ASN cc_start: 0.8112 (m-40) cc_final: 0.7788 (p0) outliers start: 28 outliers final: 17 residues processed: 317 average time/residue: 0.5087 time to fit residues: 274.9185 Evaluate side-chains 276 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 258 time to evaluate : 4.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 1036 CYS Chi-restraints excluded: chain D residue 1142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 269 optimal weight: 6.9990 chunk 150 optimal weight: 0.0020 chunk 403 optimal weight: 4.9990 chunk 330 optimal weight: 0.0370 chunk 133 optimal weight: 9.9990 chunk 485 optimal weight: 4.9990 chunk 524 optimal weight: 7.9990 chunk 432 optimal weight: 1.9990 chunk 481 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 389 optimal weight: 6.9990 overall best weight: 2.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 346 HIS ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 HIS ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN G 298 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 ASN ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 44032 Z= 0.321 Angle : 0.610 7.431 59537 Z= 0.309 Chirality : 0.042 0.163 6754 Planarity : 0.003 0.048 7543 Dihedral : 6.523 108.559 5932 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.46 % Favored : 91.32 % Rotamer: Outliers : 1.21 % Allowed : 8.60 % Favored : 90.19 % 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: -1.09 (0.12), residues: 5360 helix: 1.01 (0.12), residues: 2144 sheet: -1.55 (0.19), residues: 824 loop : -2.06 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 992 HIS 0.010 0.001 HIS C 346 PHE 0.020 0.001 PHE D 959 TYR 0.016 0.001 TYR G 179 ARG 0.005 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 265 time to evaluate : 5.014 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: A 795 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.8007 (mp10) REVERT: A 837 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9163 (p) REVERT: A 976 ILE cc_start: 0.8943 (mp) cc_final: 0.8726 (tp) REVERT: A 1009 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7293 (p0) REVERT: A 1052 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8358 (mtpt) REVERT: B 422 ASP cc_start: 0.8452 (t70) cc_final: 0.8107 (t0) REVERT: B 622 LYS cc_start: 0.9588 (mmpt) cc_final: 0.9372 (mmmt) REVERT: B 1005 ASN cc_start: 0.8365 (t0) cc_final: 0.8150 (t0) REVERT: B 1062 MET cc_start: 0.8996 (mtm) cc_final: 0.8708 (mtm) REVERT: C 343 MET cc_start: 0.9497 (tpp) cc_final: 0.9279 (tpp) REVERT: C 984 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8648 (mmtm) REVERT: C 1052 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8675 (mtpt) REVERT: C 1062 MET cc_start: 0.8913 (mtm) cc_final: 0.8624 (mtm) REVERT: H 301 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8893 (tm-30) REVERT: G 219 ILE cc_start: 0.9513 (tp) cc_final: 0.9291 (tp) REVERT: D 1005 ASN cc_start: 0.8176 (m-40) cc_final: 0.7799 (p0) REVERT: D 1027 ASN cc_start: 0.8752 (t0) cc_final: 0.8541 (t0) outliers start: 52 outliers final: 29 residues processed: 307 average time/residue: 0.5161 time to fit residues: 274.5618 Evaluate side-chains 282 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 795 GLN Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1035 ASP Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 479 optimal weight: 4.9990 chunk 365 optimal weight: 0.9980 chunk 252 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 chunk 326 optimal weight: 0.0980 chunk 487 optimal weight: 3.9990 chunk 516 optimal weight: 0.0370 chunk 254 optimal weight: 0.9990 chunk 462 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN B 336 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN H 277 GLN ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 44032 Z= 0.141 Angle : 0.540 11.958 59537 Z= 0.273 Chirality : 0.040 0.156 6754 Planarity : 0.003 0.044 7543 Dihedral : 6.143 113.978 5932 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.67 % Favored : 93.11 % Rotamer: Outliers : 1.31 % Allowed : 9.60 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 5360 helix: 1.17 (0.12), residues: 2146 sheet: -1.48 (0.18), residues: 844 loop : -1.96 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 992 HIS 0.004 0.001 HIS A 439 PHE 0.015 0.001 PHE D 959 TYR 0.009 0.001 TYR A 611 ARG 0.005 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 285 time to evaluate : 5.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8438 (mt0) REVERT: A 601 ARG cc_start: 0.7865 (tpt90) cc_final: 0.7361 (tpt90) REVERT: A 622 LYS cc_start: 0.9145 (pttm) cc_final: 0.8892 (pptt) REVERT: A 795 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7976 (mp10) REVERT: A 818 TRP cc_start: 0.8176 (t60) cc_final: 0.7238 (t60) REVERT: A 976 ILE cc_start: 0.8901 (mp) cc_final: 0.8679 (tp) REVERT: A 1052 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8454 (mtpt) REVERT: B 280 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8591 (t) REVERT: B 422 ASP cc_start: 0.8373 (t70) cc_final: 0.7970 (t0) REVERT: B 1005 ASN cc_start: 0.8410 (t0) cc_final: 0.8147 (t0) REVERT: B 1062 MET cc_start: 0.8971 (mtm) cc_final: 0.8701 (mtm) REVERT: B 1124 MET cc_start: 0.8616 (ttp) cc_final: 0.8319 (ttp) REVERT: C 818 TRP cc_start: 0.8062 (t60) cc_final: 0.7166 (t60) REVERT: C 984 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8627 (mmtm) REVERT: C 1052 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8637 (mtpt) REVERT: C 1062 MET cc_start: 0.8862 (mtm) cc_final: 0.8586 (mtm) REVERT: C 1140 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8393 (pp30) REVERT: F 240 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8639 (mmmt) REVERT: D 280 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8609 (t) REVERT: D 992 TRP cc_start: 0.7262 (OUTLIER) cc_final: 0.5716 (p90) REVERT: D 1005 ASN cc_start: 0.8105 (m-40) cc_final: 0.7817 (p0) outliers start: 57 outliers final: 19 residues processed: 330 average time/residue: 0.5813 time to fit residues: 336.6048 Evaluate side-chains 287 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 262 time to evaluate : 5.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 795 GLN Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 1142 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 429 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 384 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 440 optimal weight: 10.0000 chunk 356 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 463 optimal weight: 0.0040 chunk 130 optimal weight: 1.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44032 Z= 0.228 Angle : 0.556 9.608 59537 Z= 0.280 Chirality : 0.041 0.203 6754 Planarity : 0.003 0.042 7543 Dihedral : 6.027 112.629 5928 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.43 % Favored : 92.35 % Rotamer: Outliers : 1.37 % Allowed : 10.39 % Favored : 88.23 % 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: -0.77 (0.12), residues: 5360 helix: 1.30 (0.12), residues: 2118 sheet: -1.39 (0.19), residues: 834 loop : -1.89 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 992 HIS 0.005 0.001 HIS B 346 PHE 0.020 0.001 PHE D 192 TYR 0.014 0.001 TYR E 230 ARG 0.004 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 273 time to evaluate : 4.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8545 (mt0) REVERT: A 622 LYS cc_start: 0.9146 (pttm) cc_final: 0.8879 (pptt) REVERT: A 976 ILE cc_start: 0.8959 (mp) cc_final: 0.8721 (tp) REVERT: A 1009 ASN cc_start: 0.7393 (OUTLIER) cc_final: 0.7167 (p0) REVERT: A 1052 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8470 (mtpt) REVERT: B 266 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8759 (mpp) REVERT: B 422 ASP cc_start: 0.8407 (t70) cc_final: 0.8038 (t0) REVERT: B 984 LYS cc_start: 0.9044 (mmpt) cc_final: 0.8517 (mmmt) REVERT: C 984 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8650 (mmtm) REVERT: C 1052 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8627 (mtpt) REVERT: E 249 GLU cc_start: 0.8760 (tp30) cc_final: 0.8370 (tp30) REVERT: E 255 MET cc_start: 0.8626 (tpp) cc_final: 0.8406 (mtp) REVERT: H 240 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8590 (mmmt) REVERT: F 240 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8623 (mmmt) REVERT: D 992 TRP cc_start: 0.7474 (OUTLIER) cc_final: 0.5879 (p90) REVERT: D 1005 ASN cc_start: 0.8133 (m-40) cc_final: 0.7765 (p0) REVERT: D 1027 ASN cc_start: 0.8795 (t0) cc_final: 0.8578 (t0) outliers start: 60 outliers final: 33 residues processed: 319 average time/residue: 0.5110 time to fit residues: 284.2865 Evaluate side-chains 298 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 261 time to evaluate : 5.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 4.9990 chunk 464 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 303 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 516 optimal weight: 0.9990 chunk 428 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS B1140 GLN ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 44032 Z= 0.255 Angle : 0.563 9.751 59537 Z= 0.284 Chirality : 0.041 0.211 6754 Planarity : 0.003 0.042 7543 Dihedral : 6.032 112.081 5928 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.64 % Favored : 92.14 % Rotamer: Outliers : 1.44 % Allowed : 10.96 % Favored : 87.61 % 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: -0.76 (0.12), residues: 5360 helix: 1.33 (0.12), residues: 2106 sheet: -1.39 (0.19), residues: 830 loop : -1.87 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 992 HIS 0.004 0.001 HIS C1157 PHE 0.021 0.001 PHE D 192 TYR 0.013 0.001 TYR G 179 ARG 0.004 0.000 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 267 time to evaluate : 5.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: A 622 LYS cc_start: 0.9147 (pttm) cc_final: 0.8865 (pptt) REVERT: A 818 TRP cc_start: 0.8164 (t60) cc_final: 0.7730 (t60) REVERT: A 976 ILE cc_start: 0.8976 (mp) cc_final: 0.8745 (tp) REVERT: A 996 MET cc_start: 0.8484 (pmm) cc_final: 0.7836 (pmm) REVERT: A 1052 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8476 (mtpt) REVERT: B 280 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8722 (t) REVERT: B 422 ASP cc_start: 0.8438 (t70) cc_final: 0.8077 (t0) REVERT: B 1062 MET cc_start: 0.8996 (mtm) cc_final: 0.8711 (mtm) REVERT: B 1124 MET cc_start: 0.8644 (ttp) cc_final: 0.8428 (ttp) REVERT: C 280 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8319 (t) REVERT: C 984 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8676 (mmtm) REVERT: C 1052 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8625 (mtpt) REVERT: C 1062 MET cc_start: 0.8858 (mtm) cc_final: 0.8600 (mtm) REVERT: H 240 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8567 (mmmt) REVERT: F 240 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8599 (mmmt) REVERT: G 249 GLU cc_start: 0.7953 (pt0) cc_final: 0.7693 (pt0) REVERT: D 280 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8764 (t) REVERT: D 992 TRP cc_start: 0.7582 (OUTLIER) cc_final: 0.5970 (p90) REVERT: D 1005 ASN cc_start: 0.8171 (m-40) cc_final: 0.7774 (p0) outliers start: 63 outliers final: 40 residues processed: 316 average time/residue: 0.4937 time to fit residues: 272.5984 Evaluate side-chains 302 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 257 time to evaluate : 5.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 906 ASN Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1173 LEU Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 498 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 294 optimal weight: 0.0570 chunk 377 optimal weight: 0.5980 chunk 292 optimal weight: 2.9990 chunk 434 optimal weight: 6.9990 chunk 288 optimal weight: 0.2980 chunk 514 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN B 628 HIS ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 GLN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 44032 Z= 0.134 Angle : 0.523 9.813 59537 Z= 0.263 Chirality : 0.040 0.176 6754 Planarity : 0.003 0.041 7543 Dihedral : 5.777 114.154 5928 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.48 % Favored : 93.30 % Rotamer: Outliers : 1.25 % Allowed : 11.29 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 5360 helix: 1.37 (0.12), residues: 2110 sheet: -1.32 (0.19), residues: 846 loop : -1.82 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP C 992 HIS 0.004 0.001 HIS C 628 PHE 0.018 0.001 PHE D 192 TYR 0.011 0.001 TYR C1119 ARG 0.003 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 284 time to evaluate : 4.942 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: A 332 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: A 530 LYS cc_start: 0.9321 (mtmt) cc_final: 0.9115 (ptmt) REVERT: A 622 LYS cc_start: 0.9150 (pttm) cc_final: 0.8877 (pptt) REVERT: A 996 MET cc_start: 0.8241 (pmm) cc_final: 0.7617 (pmm) REVERT: A 1052 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8426 (mtpt) REVERT: B 280 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8598 (t) REVERT: B 422 ASP cc_start: 0.8319 (t70) cc_final: 0.7969 (t0) REVERT: B 837 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.9092 (p) REVERT: B 1124 MET cc_start: 0.8566 (ttp) cc_final: 0.8362 (ttp) REVERT: C 818 TRP cc_start: 0.8022 (t60) cc_final: 0.7806 (t60) REVERT: C 984 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8639 (mmtm) REVERT: C 1052 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8580 (mtpt) REVERT: C 1062 MET cc_start: 0.8800 (mtm) cc_final: 0.8531 (mtm) REVERT: H 240 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8555 (mmmt) REVERT: F 240 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8604 (mmmt) REVERT: G 240 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8380 (mmmt) REVERT: G 249 GLU cc_start: 0.7884 (pt0) cc_final: 0.7497 (pt0) REVERT: D 280 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8629 (t) REVERT: D 992 TRP cc_start: 0.7472 (OUTLIER) cc_final: 0.6185 (p90) REVERT: D 1005 ASN cc_start: 0.8102 (m-40) cc_final: 0.7840 (p0) REVERT: D 1062 MET cc_start: 0.8768 (mtm) cc_final: 0.8423 (mtm) outliers start: 54 outliers final: 29 residues processed: 331 average time/residue: 0.5151 time to fit residues: 295.9447 Evaluate side-chains 301 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 267 time to evaluate : 5.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 992 TRP Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 318 optimal weight: 0.0020 chunk 205 optimal weight: 0.4980 chunk 307 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 327 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 404 optimal weight: 0.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 44032 Z= 0.164 Angle : 0.529 11.976 59537 Z= 0.266 Chirality : 0.040 0.271 6754 Planarity : 0.003 0.040 7543 Dihedral : 5.729 114.089 5928 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.68 % Favored : 93.09 % Rotamer: Outliers : 1.19 % Allowed : 11.77 % Favored : 87.04 % 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: -0.61 (0.12), residues: 5360 helix: 1.43 (0.12), residues: 2108 sheet: -1.26 (0.19), residues: 850 loop : -1.79 (0.13), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP C 992 HIS 0.006 0.001 HIS C 580 PHE 0.024 0.001 PHE D 192 TYR 0.031 0.001 TYR G 310 ARG 0.003 0.000 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 275 time to evaluate : 4.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9043 (tmm) cc_final: 0.8743 (tmm) REVERT: A 622 LYS cc_start: 0.9152 (pttm) cc_final: 0.8886 (pptt) REVERT: A 976 ILE cc_start: 0.9002 (tp) cc_final: 0.8704 (tp) REVERT: A 996 MET cc_start: 0.8244 (pmm) cc_final: 0.7621 (pmm) REVERT: A 1052 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8427 (mtpt) REVERT: B 280 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8640 (t) REVERT: B 422 ASP cc_start: 0.8357 (t70) cc_final: 0.8030 (t0) REVERT: B 1062 MET cc_start: 0.8969 (mtm) cc_final: 0.8722 (mtm) REVERT: C 253 SER cc_start: 0.8997 (t) cc_final: 0.8786 (p) REVERT: C 818 TRP cc_start: 0.8014 (t60) cc_final: 0.7754 (t60) REVERT: C 984 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8659 (mmtm) REVERT: C 1052 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8581 (mtpt) REVERT: C 1062 MET cc_start: 0.8847 (mtm) cc_final: 0.8607 (mtm) REVERT: C 1119 TYR cc_start: 0.6109 (p90) cc_final: 0.5902 (p90) REVERT: H 240 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8566 (mmmt) REVERT: F 240 LYS cc_start: 0.8866 (mmtm) cc_final: 0.8589 (mmmt) REVERT: G 240 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8363 (mmmt) REVERT: G 249 GLU cc_start: 0.7909 (pt0) cc_final: 0.7524 (pt0) REVERT: D 280 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8712 (t) REVERT: D 1005 ASN cc_start: 0.8107 (m-40) cc_final: 0.7775 (p0) REVERT: D 1062 MET cc_start: 0.8745 (mtm) cc_final: 0.8503 (mtm) outliers start: 51 outliers final: 37 residues processed: 316 average time/residue: 0.5103 time to fit residues: 278.9147 Evaluate side-chains 300 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 261 time to evaluate : 5.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 906 ASN Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 468 optimal weight: 0.4980 chunk 493 optimal weight: 0.8980 chunk 449 optimal weight: 5.9990 chunk 479 optimal weight: 9.9990 chunk 492 optimal weight: 3.9990 chunk 288 optimal weight: 0.5980 chunk 208 optimal weight: 0.3980 chunk 376 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 433 optimal weight: 5.9990 chunk 453 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44032 Z= 0.139 Angle : 0.525 10.595 59537 Z= 0.263 Chirality : 0.040 0.173 6754 Planarity : 0.003 0.047 7543 Dihedral : 5.618 113.531 5926 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.03 % Favored : 93.75 % Rotamer: Outliers : 1.06 % Allowed : 11.87 % Favored : 87.07 % 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: -0.55 (0.12), residues: 5360 helix: 1.48 (0.12), residues: 2100 sheet: -1.19 (0.19), residues: 844 loop : -1.77 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 992 HIS 0.004 0.001 HIS B1157 PHE 0.013 0.001 PHE B 250 TYR 0.045 0.001 TYR G 310 ARG 0.007 0.000 ARG E 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 282 time to evaluate : 5.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9020 (tmm) cc_final: 0.8720 (tmm) REVERT: A 622 LYS cc_start: 0.9162 (pttm) cc_final: 0.8898 (pptt) REVERT: A 976 ILE cc_start: 0.8967 (tp) cc_final: 0.8696 (tp) REVERT: A 996 MET cc_start: 0.8258 (pmm) cc_final: 0.7684 (pmm) REVERT: A 1052 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8414 (mtpt) REVERT: B 280 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (t) REVERT: B 422 ASP cc_start: 0.8346 (t70) cc_final: 0.8007 (t0) REVERT: B 837 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9048 (p) REVERT: B 1062 MET cc_start: 0.8951 (mtm) cc_final: 0.8716 (mtm) REVERT: C 253 SER cc_start: 0.8976 (t) cc_final: 0.8760 (p) REVERT: C 339 MET cc_start: 0.9072 (tmm) cc_final: 0.8703 (tmm) REVERT: C 601 ARG cc_start: 0.7678 (tpt90) cc_final: 0.7221 (tpt90) REVERT: C 818 TRP cc_start: 0.7984 (t60) cc_final: 0.7731 (t60) REVERT: C 837 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9149 (p) REVERT: C 984 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8648 (mmtm) REVERT: C 1052 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8566 (mtpt) REVERT: C 1062 MET cc_start: 0.8834 (mtm) cc_final: 0.8592 (mtm) REVERT: H 240 LYS cc_start: 0.8861 (mmtm) cc_final: 0.8523 (mmmt) REVERT: F 240 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8623 (mmmt) REVERT: G 240 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8354 (mmmt) REVERT: G 249 GLU cc_start: 0.7923 (pt0) cc_final: 0.7555 (pt0) REVERT: D 280 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8678 (t) REVERT: D 1005 ASN cc_start: 0.8089 (m-40) cc_final: 0.7861 (p0) outliers start: 45 outliers final: 34 residues processed: 320 average time/residue: 0.5119 time to fit residues: 285.2594 Evaluate side-chains 305 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 267 time to evaluate : 5.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 477 optimal weight: 10.0000 chunk 314 optimal weight: 0.5980 chunk 507 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 532 optimal weight: 2.9990 chunk 489 optimal weight: 5.9990 chunk 423 optimal weight: 0.0050 chunk 43 optimal weight: 2.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1015 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 44032 Z= 0.238 Angle : 0.560 10.202 59537 Z= 0.281 Chirality : 0.041 0.260 6754 Planarity : 0.003 0.040 7543 Dihedral : 5.725 111.716 5926 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.24 % Favored : 92.53 % Rotamer: Outliers : 1.06 % Allowed : 12.23 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 5360 helix: 1.55 (0.12), residues: 2098 sheet: -1.20 (0.19), residues: 846 loop : -1.77 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 992 HIS 0.006 0.001 HIS A 439 PHE 0.011 0.001 PHE D 959 TYR 0.019 0.001 TYR B1119 ARG 0.008 0.000 ARG E 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 267 time to evaluate : 5.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9053 (tmm) cc_final: 0.8737 (tmm) REVERT: A 622 LYS cc_start: 0.9170 (pttm) cc_final: 0.8890 (pptt) REVERT: A 976 ILE cc_start: 0.9055 (tp) cc_final: 0.8808 (tp) REVERT: A 996 MET cc_start: 0.8308 (pmm) cc_final: 0.7631 (pmm) REVERT: A 1052 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8435 (mtpt) REVERT: B 280 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8754 (t) REVERT: B 422 ASP cc_start: 0.8401 (t70) cc_final: 0.8088 (t0) REVERT: B 1062 MET cc_start: 0.8982 (mtm) cc_final: 0.8719 (mtm) REVERT: C 339 MET cc_start: 0.9098 (tmm) cc_final: 0.8713 (tmm) REVERT: C 601 ARG cc_start: 0.7572 (tpt90) cc_final: 0.7109 (tpt90) REVERT: C 818 TRP cc_start: 0.8039 (t60) cc_final: 0.7813 (t60) REVERT: C 984 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8693 (mmtm) REVERT: C 1052 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8601 (mtpt) REVERT: H 240 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8503 (mmmt) REVERT: F 240 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8580 (mmmt) REVERT: G 240 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8323 (mmmt) REVERT: G 249 GLU cc_start: 0.7945 (pt0) cc_final: 0.7594 (pt0) REVERT: D 280 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8786 (t) REVERT: D 1005 ASN cc_start: 0.8157 (m-40) cc_final: 0.7769 (p0) outliers start: 45 outliers final: 37 residues processed: 305 average time/residue: 0.5131 time to fit residues: 272.9361 Evaluate side-chains 301 residues out of total 4856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 262 time to evaluate : 4.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 992 TRP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1173 LEU Chi-restraints excluded: chain B residue 1192 ILE Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 999 LEU Chi-restraints excluded: chain C residue 1142 THR Chi-restraints excluded: chain C residue 1173 LEU Chi-restraints excluded: chain C residue 1192 ILE Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain D residue 638 LYS Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 1109 CYS Chi-restraints excluded: chain D residue 1142 THR Chi-restraints excluded: chain D residue 1192 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 259 optimal weight: 0.0000 chunk 336 optimal weight: 3.9990 chunk 451 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 390 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 424 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 435 optimal weight: 6.9990 chunk 53 optimal weight: 0.0870 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN A1140 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1015 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.069821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053811 restraints weight = 195706.599| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 4.70 r_work: 0.2987 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44032 Z= 0.136 Angle : 0.534 12.264 59537 Z= 0.265 Chirality : 0.040 0.238 6754 Planarity : 0.003 0.044 7543 Dihedral : 5.587 111.301 5926 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.09 % Favored : 93.69 % Rotamer: Outliers : 1.12 % Allowed : 12.16 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 5360 helix: 1.56 (0.12), residues: 2088 sheet: -1.13 (0.19), residues: 846 loop : -1.73 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 818 HIS 0.004 0.001 HIS A 439 PHE 0.012 0.001 PHE B 250 TYR 0.010 0.001 TYR E 230 ARG 0.007 0.000 ARG E 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9074.46 seconds wall clock time: 165 minutes 46.75 seconds (9946.75 seconds total)