Starting phenix.real_space_refine on Sat Mar 7 00:37:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5b_33615/03_2026/7y5b_33615.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5b_33615/03_2026/7y5b_33615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y5b_33615/03_2026/7y5b_33615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5b_33615/03_2026/7y5b_33615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5b_33615/03_2026/7y5b_33615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5b_33615/03_2026/7y5b_33615.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 106 5.16 5 C 22813 2.51 5 N 6242 2.21 5 O 6776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35959 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3843 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 495} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 9} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3790 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 3822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3822 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 22, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 11, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3503 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3508 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3528 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2220 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 32 Chain: "a" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1604 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1055 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 141} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "d" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3010 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 11, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 11, 'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 144 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 552 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "3" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 548 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "5" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "6" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "7" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "8" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 573 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 78} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "9" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.06, per 1000 atoms: 0.22 Number of scatterers: 35959 At special positions: 0 Unit cell: (180.4, 123.2, 233.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 17 15.00 Mg 5 11.99 O 6776 8.00 N 6242 7.00 C 22813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 29 sheets defined 58.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.543A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.746A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 3.592A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 299 No H-bonds generated for 'chain 'A' and resid 298 through 299' Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.924A pdb=" N GLU A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.915A pdb=" N PHE A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.540A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.205A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 407 removed outlier: 4.124A pdb=" N ASP A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 454 through 459 removed outlier: 4.400A pdb=" N SER A 458 " --> pdb=" O HIS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.661A pdb=" N PHE A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.942A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.368A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.616A pdb=" N ASP B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 195 removed outlier: 4.090A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.844A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.613A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.531A pdb=" N ALA B 296 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 311 removed outlier: 4.128A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.944A pdb=" N PHE B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.636A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 392 through 404 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 431 Processing helix chain 'B' and resid 440 through 454 removed outlier: 3.527A pdb=" N GLY B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 458 removed outlier: 4.244A pdb=" N SER B 458 " --> pdb=" O HIS B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 458' Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 493 through 510 removed outlier: 3.628A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.858A pdb=" N UNK C 22 " --> pdb=" O UNK C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.870A pdb=" N PHE C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 107 " --> pdb=" O ASP C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.667A pdb=" N ASP C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.219A pdb=" N VAL C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 264 removed outlier: 3.839A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Proline residue: C 250 - end of helix removed outlier: 3.743A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.646A pdb=" N THR C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 removed outlier: 3.638A pdb=" N ASP C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.549A pdb=" N LEU C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 476 removed outlier: 3.972A pdb=" N GLU C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.686A pdb=" N ASP C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 181 removed outlier: 3.660A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 223 through 246 removed outlier: 3.935A pdb=" N ARG D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 270 removed outlier: 3.512A pdb=" N LEU D 270 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 292 removed outlier: 3.529A pdb=" N GLU D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 removed outlier: 4.255A pdb=" N ASP D 313 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 324 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 362 through 389 removed outlier: 4.541A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 413 removed outlier: 4.089A pdb=" N SER D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 431 through 443 Processing helix chain 'D' and resid 444 through 450 removed outlier: 6.317A pdb=" N PHE D 447 " --> pdb=" O LYS D 444 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP D 448 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS D 449 " --> pdb=" O GLU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 removed outlier: 3.741A pdb=" N PHE D 456 " --> pdb=" O GLN D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.832A pdb=" N VAL E 94 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS E 95 " --> pdb=" O ASP E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 91 through 95' Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 141 through 148 removed outlier: 3.816A pdb=" N ASP E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 181 removed outlier: 3.741A pdb=" N LEU E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.762A pdb=" N ARG E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 271 removed outlier: 3.884A pdb=" N THR E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 292 Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.980A pdb=" N ASP E 313 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 324 removed outlier: 3.606A pdb=" N ALA E 321 " --> pdb=" O ASP E 317 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 334 through 341 removed outlier: 3.615A pdb=" N GLY E 341 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 387 removed outlier: 3.522A pdb=" N TYR E 366 " --> pdb=" O GLY E 362 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 412 removed outlier: 4.381A pdb=" N LEU E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 412 " --> pdb=" O ILE E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.554A pdb=" N GLY E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 450 removed outlier: 4.135A pdb=" N HIS E 449 " --> pdb=" O GLU E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.512A pdb=" N ALA E 454 " --> pdb=" O PRO E 451 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE E 456 " --> pdb=" O GLN E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 126 through 130 removed outlier: 3.553A pdb=" N ASP F 129 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 130 " --> pdb=" O PHE F 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 126 through 130' Processing helix chain 'F' and resid 141 through 147 Processing helix chain 'F' and resid 165 through 179 removed outlier: 4.121A pdb=" N ARG F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 removed outlier: 3.524A pdb=" N GLY F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 211 removed outlier: 3.757A pdb=" N LYS F 211 " --> pdb=" O ASN F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 223 through 228 removed outlier: 3.868A pdb=" N ARG F 227 " --> pdb=" O PRO F 223 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET F 228 " --> pdb=" O PRO F 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 223 through 228' Processing helix chain 'F' and resid 229 through 246 removed outlier: 3.653A pdb=" N GLU F 244 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 271 removed outlier: 3.827A pdb=" N THR F 260 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 269 " --> pdb=" O GLU F 265 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 282 through 292 removed outlier: 3.556A pdb=" N GLU F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 314 removed outlier: 4.297A pdb=" N ASP F 313 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 325 removed outlier: 4.087A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 341 removed outlier: 3.766A pdb=" N PHE F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 390 removed outlier: 3.699A pdb=" N TYR F 366 " --> pdb=" O GLY F 362 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 394 Processing helix chain 'F' and resid 395 through 412 Processing helix chain 'F' and resid 416 through 421 removed outlier: 4.068A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 445 removed outlier: 3.738A pdb=" N THR F 435 " --> pdb=" O PRO F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 456 removed outlier: 3.547A pdb=" N PHE F 456 " --> pdb=" O GLN F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 470 Processing helix chain 'G' and resid 5 through 41 removed outlier: 3.998A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 60 removed outlier: 4.235A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 109 removed outlier: 3.757A pdb=" N ASP G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.749A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 176 Processing helix chain 'G' and resid 227 through 302 Proline residue: G 237 - end of helix removed outlier: 3.809A pdb=" N LEU G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU G 249 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG G 261 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET G 263 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU G 273 " --> pdb=" O ASN G 269 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 removed outlier: 3.851A pdb=" N SER H 101 " --> pdb=" O GLU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'a' and resid 33 through 53 removed outlier: 3.812A pdb=" N ALA a 51 " --> pdb=" O PHE a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.593A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.973A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA a 148 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG a 153 " --> pdb=" O GLY a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 Processing helix chain 'a' and resid 170 through 206 Proline residue: a 182 - end of helix removed outlier: 4.438A pdb=" N PHE a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 246 removed outlier: 3.622A pdb=" N THR a 220 " --> pdb=" O ALA a 216 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU a 246 " --> pdb=" O SER a 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 48 removed outlier: 3.970A pdb=" N LEU b 35 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 59 removed outlier: 4.086A pdb=" N ILE b 53 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS b 55 " --> pdb=" O PRO b 51 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL b 56 " --> pdb=" O PRO b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 145 removed outlier: 3.834A pdb=" N MET b 63 " --> pdb=" O GLU b 59 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU b 64 " --> pdb=" O ARG b 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG b 72 " --> pdb=" O ALA b 68 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER b 74 " --> pdb=" O ASP b 70 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA b 75 " --> pdb=" O ASN b 71 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER b 134 " --> pdb=" O ASP b 130 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN b 139 " --> pdb=" O ALA b 135 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 161 Processing helix chain 'd' and resid 3 through 18 removed outlier: 4.131A pdb=" N ILE d 9 " --> pdb=" O ILE d 5 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY d 10 " --> pdb=" O GLY d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 54 removed outlier: 3.689A pdb=" N VAL d 26 " --> pdb=" O VAL d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 136 removed outlier: 4.431A pdb=" N LYS d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 157 removed outlier: 3.868A pdb=" N GLN d 143 " --> pdb=" O ASP d 139 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER d 144 " --> pdb=" O PRO d 140 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 191 Processing helix chain 'd' and resid 197 through 216 removed outlier: 3.546A pdb=" N GLU d 216 " --> pdb=" O LEU d 212 " (cutoff:3.500A) Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 230 through 240 Processing helix chain 'd' and resid 246 through 259 Processing helix chain 'd' and resid 263 through 285 removed outlier: 4.136A pdb=" N VAL d 271 " --> pdb=" O LEU d 267 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU d 272 " --> pdb=" O ILE d 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 306 removed outlier: 3.615A pdb=" N GLU d 306 " --> pdb=" O VAL d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 313 removed outlier: 3.656A pdb=" N SER d 310 " --> pdb=" O GLU d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 321 through 331 Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 372 removed outlier: 4.019A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 386 through 401 Processing helix chain 'd' and resid 431 through 442 Processing helix chain '1' and resid 6 through 46 removed outlier: 4.014A pdb=" N ALA 1 44 " --> pdb=" O ILE 1 40 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG 1 45 " --> pdb=" O SER 1 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN 1 46 " --> pdb=" O GLY 1 42 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 52 Processing helix chain '1' and resid 53 through 81 removed outlier: 3.574A pdb=" N PHE 1 57 " --> pdb=" O LEU 1 53 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL 1 64 " --> pdb=" O THR 1 60 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 50 through 79 removed outlier: 4.249A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 48 through 52 removed outlier: 4.064A pdb=" N GLY 3 51 " --> pdb=" O GLU 3 48 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG 3 52 " --> pdb=" O ALA 3 49 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 48 through 52' Processing helix chain '3' and resid 53 through 81 removed outlier: 3.906A pdb=" N PHE 3 57 " --> pdb=" O LEU 3 53 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE 3 80 " --> pdb=" O ALA 3 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA 3 81 " --> pdb=" O LEU 3 77 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 54 through 79 removed outlier: 3.925A pdb=" N PHE 4 58 " --> pdb=" O PHE 4 54 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA 4 67 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR 4 68 " --> pdb=" O VAL 4 64 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU 4 77 " --> pdb=" O ALA 4 73 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE 4 78 " --> pdb=" O PHE 4 74 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 43 removed outlier: 3.830A pdb=" N ILE 5 43 " --> pdb=" O LEU 5 39 " (cutoff:3.500A) Processing helix chain '5' and resid 54 through 81 removed outlier: 3.648A pdb=" N ALA 5 81 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing helix chain '6' and resid 6 through 44 Processing helix chain '6' and resid 53 through 81 removed outlier: 3.634A pdb=" N LEU 6 63 " --> pdb=" O ILE 6 59 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL 6 64 " --> pdb=" O THR 6 60 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA 6 81 " --> pdb=" O LEU 6 77 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 46 removed outlier: 4.124A pdb=" N THR 7 10 " --> pdb=" O ASN 7 6 " (cutoff:3.500A) Processing helix chain '7' and resid 53 through 81 removed outlier: 3.569A pdb=" N PHE 7 57 " --> pdb=" O LEU 7 53 " (cutoff:3.500A) Processing helix chain '8' and resid 4 through 44 removed outlier: 4.098A pdb=" N ILE 8 8 " --> pdb=" O ASP 8 4 " (cutoff:3.500A) Processing helix chain '8' and resid 49 through 52 Processing helix chain '8' and resid 53 through 82 removed outlier: 3.864A pdb=" N PHE 8 57 " --> pdb=" O LEU 8 53 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU 8 63 " --> pdb=" O ILE 8 59 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL 8 64 " --> pdb=" O THR 8 60 " (cutoff:3.500A) Processing helix chain '9' and resid 8 through 46 removed outlier: 4.354A pdb=" N GLY 9 12 " --> pdb=" O ILE 9 8 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN 9 46 " --> pdb=" O GLY 9 42 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 4.049A pdb=" N GLU A 29 " --> pdb=" O VAL d 427 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL d 379 " --> pdb=" O HIS d 410 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 36 removed outlier: 6.782A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 42 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY A 64 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.861A pdb=" N ALA A 236 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 233 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 268 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 270 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 325 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 271 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 171 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.665A pdb=" N GLU B 45 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 57 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 92 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 102 removed outlier: 3.646A pdb=" N ARG B 130 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 128 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.414A pdb=" N VAL B 111 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 330 removed outlier: 6.440A pdb=" N ILE B 170 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 33 through 38 removed outlier: 6.432A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 36 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU C 69 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 66 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 94 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 92 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.691A pdb=" N THR C 128 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.364A pdb=" N VAL C 111 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG C 203 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL C 270 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 205 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 271 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.302A pdb=" N ILE C 170 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 171 " --> pdb=" O CYS C 353 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 534 through 535 removed outlier: 6.165A pdb=" N GLU C 534 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA G 77 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N TRP G 138 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL G 118 " --> pdb=" O TRP G 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 538 through 540 removed outlier: 6.501A pdb=" N VAL C 538 " --> pdb=" O GLU G 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 16 removed outlier: 5.684A pdb=" N VAL D 12 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU D 23 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG D 14 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D 20 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N HIS D 56 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 54 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS D 47 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS D 37 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU D 39 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU D 78 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 87 through 90 Processing sheet with id=AB8, first strand: chain 'D' and resid 98 through 99 removed outlier: 3.749A pdb=" N PHE D 217 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 214 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 250 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 156 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 329 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 352 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 136 through 137 removed outlier: 4.530A pdb=" N TYR D 150 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 16 removed outlier: 5.566A pdb=" N VAL E 12 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU E 23 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG E 14 " --> pdb=" O ASP E 21 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS E 56 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 47 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU E 39 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLU E 78 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 99 removed outlier: 3.575A pdb=" N THR E 303 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 136 through 137 removed outlier: 3.792A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 306 through 308 removed outlier: 6.293A pdb=" N ILE E 156 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL E 308 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU E 158 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 11 through 16 removed outlier: 3.864A pdb=" N VAL F 13 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS F 47 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE F 40 " --> pdb=" O LYS F 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 87 through 89 removed outlier: 3.610A pdb=" N VAL F 88 " --> pdb=" O TRP F 118 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP F 118 " --> pdb=" O VAL F 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.418A pdb=" N PHE F 99 " --> pdb=" O PHE F 217 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE F 156 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS F 155 " --> pdb=" O ALA F 329 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 136 through 137 removed outlier: 3.656A pdb=" N LEU F 137 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 14 through 19 removed outlier: 4.507A pdb=" N TRP H 16 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG H 78 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER H 71 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 31 through 33 removed outlier: 3.613A pdb=" N THR H 25 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA H 64 " --> pdb=" O GLN H 85 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN H 85 " --> pdb=" O ALA H 64 " (cutoff:3.500A) 2166 hydrogen bonds defined for protein. 6345 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: 7.47 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8329 1.33 - 1.45: 7032 1.45 - 1.57: 20978 1.57 - 1.69: 28 1.69 - 1.82: 192 Bond restraints: 36559 Sorted by residual: bond pdb=" N LYS D 95 " pdb=" CA LYS D 95 " ideal model delta sigma weight residual 1.458 1.476 -0.018 1.35e-02 5.49e+03 1.72e+00 bond pdb=" CD GLN d 86 " pdb=" OE1 GLN d 86 " ideal model delta sigma weight residual 1.231 1.209 0.022 1.90e-02 2.77e+03 1.31e+00 bond pdb=" CD GLU d 96 " pdb=" OE1 GLU d 96 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.29e+00 bond pdb=" CA ASP G 271 " pdb=" C ASP G 271 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.30e-02 5.92e+03 1.27e+00 bond pdb=" C THR G 267 " pdb=" O THR G 267 " ideal model delta sigma weight residual 1.237 1.250 -0.013 1.17e-02 7.31e+03 1.25e+00 ... (remaining 36554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 48892 1.83 - 3.66: 585 3.66 - 5.48: 117 5.48 - 7.31: 39 7.31 - 9.14: 8 Bond angle restraints: 49641 Sorted by residual: angle pdb=" N GLN d 86 " pdb=" CA GLN d 86 " pdb=" CB GLN d 86 " ideal model delta sigma weight residual 110.28 116.82 -6.54 1.55e+00 4.16e-01 1.78e+01 angle pdb=" C ALA d 95 " pdb=" N GLU d 96 " pdb=" CA GLU d 96 " ideal model delta sigma weight residual 120.72 114.24 6.48 1.67e+00 3.59e-01 1.50e+01 angle pdb=" N GLU d 96 " pdb=" CA GLU d 96 " pdb=" CB GLU d 96 " ideal model delta sigma weight residual 110.39 116.83 -6.44 1.66e+00 3.63e-01 1.50e+01 angle pdb=" C VAL D 94 " pdb=" N LYS D 95 " pdb=" CA LYS D 95 " ideal model delta sigma weight residual 123.47 129.17 -5.70 1.53e+00 4.27e-01 1.39e+01 angle pdb=" C ILE a 71 " pdb=" N GLN a 72 " pdb=" CA GLN a 72 " ideal model delta sigma weight residual 120.31 114.77 5.54 1.52e+00 4.33e-01 1.33e+01 ... (remaining 49636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.85: 20746 26.85 - 53.69: 1012 53.69 - 80.54: 104 80.54 - 107.38: 20 107.38 - 134.23: 1 Dihedral angle restraints: 21883 sinusoidal: 8258 harmonic: 13625 Sorted by residual: dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual 300.00 165.77 134.23 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" O2A ADP D 601 " pdb=" O3A ADP D 601 " pdb=" PA ADP D 601 " pdb=" PB ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 -134.32 74.32 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" CA ASP E 114 " pdb=" CB ASP E 114 " pdb=" CG ASP E 114 " pdb=" OD1 ASP E 114 " ideal model delta sinusoidal sigma weight residual -30.00 -87.80 57.80 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 21880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3899 0.032 - 0.064: 1292 0.064 - 0.097: 430 0.097 - 0.129: 187 0.129 - 0.161: 18 Chirality restraints: 5826 Sorted by residual: chirality pdb=" CA THR 1 55 " pdb=" N THR 1 55 " pdb=" C THR 1 55 " pdb=" CB THR 1 55 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA THR 3 55 " pdb=" N THR 3 55 " pdb=" C THR 3 55 " pdb=" CB THR 3 55 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA THR 2 55 " pdb=" N THR 2 55 " pdb=" C THR 2 55 " pdb=" CB THR 2 55 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.09e-01 ... (remaining 5823 not shown) Planarity restraints: 6454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 112 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.45e+00 pdb=" N PRO A 113 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY 9 29 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C GLY 9 29 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY 9 29 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE 9 30 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 9 32 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASP 9 32 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP 9 32 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY 9 33 " -0.013 2.00e-02 2.50e+03 ... (remaining 6451 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 154 2.49 - 3.09: 26143 3.09 - 3.70: 54112 3.70 - 4.30: 69283 4.30 - 4.90: 115995 Nonbonded interactions: 265687 Sorted by model distance: nonbonded pdb=" O1B ATP F 601 " pdb="MG MG F 602 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR F 167 " pdb="MG MG F 602 " model vdw 1.963 2.170 nonbonded pdb=" O3G ATP F 601 " pdb="MG MG F 602 " model vdw 1.980 2.170 nonbonded pdb=" O3A ATP B 601 " pdb="MG MG B 602 " model vdw 1.982 2.170 nonbonded pdb=" O1G ATP A 601 " pdb="MG MG A 602 " model vdw 1.984 2.170 ... (remaining 265682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '2' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 84)) selection = (chain '3' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '4' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '6' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '7' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '8' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '9' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) } ncs_group { reference = (chain 'A' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 132 or (resid 133 and (name N or name CA or name C or nam \ e O or name CB )) or resid 134 through 355 or (resid 356 and (name N or name CA \ or name C or name O or name CB )) or resid 357 or (resid 358 and (name N or name \ CA or name C or name O or name CB )) or resid 359 through 400 or (resid 401 thr \ ough 402 and (name N or name CA or name C or name O or name CB )) or resid 403 t \ hrough 411 or (resid 412 and (name N or name CA or name C or name O or name CB ) \ ) or resid 413 through 416 or (resid 417 through 419 and (name N or name CA or n \ ame C or name O or name CB )) or resid 420 through 461 or (resid 462 through 463 \ and (name N or name CA or name C or name O or name CB )) or resid 464 through 4 \ 67 or (resid 468 and (name N or name CA or name C or name O or name CB )) or res \ id 469 or (resid 470 and (name N or name CA or name C or name O or name CB )) or \ resid 471 through 494 or (resid 495 through 499 and (name N or name CA or name \ C or name O or name CB )) or resid 500 through 505 or (resid 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 through 516 or resid 518 \ through 602)) selection = (chain 'B' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 132 or (resid 133 and (name N or name CA or name C or nam \ e O or name CB )) or resid 134 through 190 or (resid 191 through 192 and (name N \ or name CA or name C or name O or name CB )) or resid 193 through 316 or (resid \ 317 through 318 and (name N or name CA or name C or name O or name CB )) or res \ id 319 through 355 or (resid 356 and (name N or name CA or name C or name O or n \ ame CB )) or resid 357 or (resid 358 and (name N or name CA or name C or name O \ or name CB )) or resid 359 through 401 or (resid 402 and (name N or name CA or n \ ame C or name O or name CB )) or resid 403 through 411 or (resid 412 and (name N \ or name CA or name C or name O or name CB )) or resid 413 through 416 or (resid \ 417 through 419 and (name N or name CA or name C or name O or name CB )) or res \ id 420 through 456 or (resid 457 and (name N or name CA or name C or name O or n \ ame CB )) or resid 458 through 467 or (resid 468 and (name N or name CA or name \ C or name O or name CB )) or resid 469 through 493 or (resid 494 through 499 and \ (name N or name CA or name C or name O or name CB )) or resid 500 through 505 o \ r (resid 506 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 07 through 516 or resid 518 through 602)) selection = (chain 'C' and (resid 29 through 190 or (resid 191 through 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 through 316 or (resid 317 t \ hrough 318 and (name N or name CA or name C or name O or name CB )) or resid 319 \ through 400 or (resid 401 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 403 through 456 or (resid 457 and (name N or name CA or \ name C or name O or name CB )) or resid 458 through 469 or (resid 470 and (name \ N or name CA or name C or name O or name CB )) or resid 471 through 493 or (res \ id 494 through 499 and (name N or name CA or name C or name O or name CB )) or r \ esid 500 through 516 or resid 537 through 538 or resid 540 or resid 601 through \ 602)) } ncs_group { reference = (chain 'D' and (resid 8 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB )) or resid 105 through 106 or (resid 107 and (name N or \ name CA or name C or name O or name CB )) or resid 108 through 198 or (resid 19 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 200 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 285 or (resid 286 and (name N or name CA or name C or name O or \ name CB )) or resid 287 through 362 or (resid 363 through 364 and (name N or nam \ e CA or name C or name O or name CB )) or resid 365 through 369 or (resid 370 th \ rough 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ through 380 or (resid 381 and (name N or name CA or name C or name O or name CB \ )) or resid 382 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 424 or (resid 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 through 471)) selection = (chain 'E' and (resid 8 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 220 or (resid 221 through 222 an \ d (name N or name CA or name C or name O or name CB )) or resid 223 through 284 \ or (resid 285 through 286 and (name N or name CA or name C or name O or name CB \ )) or resid 287 through 288 or (resid 289 and (name N or name CA or name C or na \ me O or name CB )) or resid 290 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 370 or (resid 371 and (n \ ame N or name CA or name C or name O or name CB )) or resid 372 through 395 or ( \ resid 396 through 398 and (name N or name CA or name C or name O or name CB )) o \ r resid 399 through 461 or (resid 462 and (name N or name CA or name C or name O \ or name CB )) or resid 463 through 465 or (resid 466 and (name N or name CA or \ name C or name O or name CB )) or resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB )) or resid 105 through 134 or (resid 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 198 or (resid 19 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 200 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 220 or (resid 221 through 222 and (name N or name CA or name C o \ r name O or name CB )) or resid 223 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 through 362 or (resid 363 th \ rough 364 and (name N or name CA or name C or name O or name CB )) or resid 365 \ through 369 or (resid 370 through 371 and (name N or name CA or name C or name O \ or name CB )) or resid 372 through 380 or (resid 381 and (name N or name CA or \ name C or name O or name CB )) or resid 382 through 383 or (resid 384 and (name \ N or name CA or name C or name O or name CB )) or resid 385 through 395 or (resi \ d 396 through 398 and (name N or name CA or name C or name O or name CB )) or re \ sid 399 through 402 or (resid 403 and (name N or name CA or name C or name O or \ name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA or name \ C or name O or name CB )) or resid 434 through 461 or (resid 462 and (name N or \ name CA or name C or name O or name CB )) or resid 463 through 465 or (resid 46 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 467 through \ 471)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 32.030 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36559 Z= 0.117 Angle : 0.557 9.140 49641 Z= 0.284 Chirality : 0.040 0.161 5826 Planarity : 0.004 0.058 6454 Dihedral : 15.008 134.229 13153 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.12), residues: 4784 helix: 2.12 (0.11), residues: 2490 sheet: 0.90 (0.24), residues: 484 loop : -1.01 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 188 TYR 0.022 0.001 TYR a 145 PHE 0.020 0.001 PHE 7 57 TRP 0.019 0.001 TRP a 218 HIS 0.005 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00230 (36559) covalent geometry : angle 0.55655 (49641) hydrogen bonds : bond 0.13842 ( 2166) hydrogen bonds : angle 5.52669 ( 6345) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 15 ILE cc_start: 0.4093 (mt) cc_final: 0.3893 (mt) REVERT: 1 58 PHE cc_start: 0.7221 (m-10) cc_final: 0.7014 (m-10) REVERT: 3 75 MET cc_start: 0.6914 (tmm) cc_final: 0.6283 (tmm) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1901 time to fit residues: 117.8831 Evaluate side-chains 260 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.0060 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 2.9990 overall best weight: 0.9738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN D 383 GLN F 55 GLN a 229 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.065732 restraints weight = 144041.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.065803 restraints weight = 106375.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.065826 restraints weight = 89435.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066175 restraints weight = 74594.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066398 restraints weight = 62342.180| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36559 Z= 0.127 Angle : 0.528 8.393 49641 Z= 0.271 Chirality : 0.040 0.222 5826 Planarity : 0.004 0.055 6454 Dihedral : 6.843 104.078 5333 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.12), residues: 4784 helix: 2.38 (0.10), residues: 2516 sheet: 0.71 (0.23), residues: 504 loop : -1.00 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 78 TYR 0.022 0.001 TYR a 145 PHE 0.015 0.001 PHE H 24 TRP 0.013 0.001 TRP E 118 HIS 0.004 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00265 (36559) covalent geometry : angle 0.52796 (49641) hydrogen bonds : bond 0.04833 ( 2166) hydrogen bonds : angle 4.26170 ( 6345) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 354 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7611 (t0) cc_final: 0.7343 (t0) REVERT: A 229 MET cc_start: 0.8297 (tpp) cc_final: 0.8061 (tpp) REVERT: D 309 TYR cc_start: 0.8390 (t80) cc_final: 0.8179 (t80) REVERT: D 355 ILE cc_start: 0.9071 (tp) cc_final: 0.8728 (tp) REVERT: 1 75 MET cc_start: 0.7751 (ppp) cc_final: 0.7482 (ppp) REVERT: 3 75 MET cc_start: 0.6982 (tmm) cc_final: 0.6429 (tmm) REVERT: 5 15 ILE cc_start: 0.5556 (mm) cc_final: 0.5284 (mm) REVERT: 5 75 MET cc_start: 0.6303 (pmm) cc_final: 0.5826 (pmm) REVERT: 9 37 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.6522 (m110) REVERT: 9 70 ILE cc_start: 0.8444 (tp) cc_final: 0.8225 (tp) outliers start: 2 outliers final: 0 residues processed: 356 average time/residue: 0.1866 time to fit residues: 117.7043 Evaluate side-chains 266 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 49 optimal weight: 0.9980 chunk 328 optimal weight: 6.9990 chunk 127 optimal weight: 0.5980 chunk 86 optimal weight: 0.0370 chunk 178 optimal weight: 4.9990 chunk 164 optimal weight: 0.2980 chunk 43 optimal weight: 0.1980 chunk 159 optimal weight: 0.0470 chunk 204 optimal weight: 3.9990 chunk 239 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN E 198 ASN F 55 GLN a 229 GLN 1 71 ASN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066845 restraints weight = 142577.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067671 restraints weight = 98155.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067652 restraints weight = 68937.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.067969 restraints weight = 62236.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068224 restraints weight = 53410.728| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36559 Z= 0.106 Angle : 0.515 10.777 49641 Z= 0.258 Chirality : 0.040 0.237 5826 Planarity : 0.004 0.049 6454 Dihedral : 6.459 93.553 5333 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.13), residues: 4784 helix: 2.49 (0.10), residues: 2513 sheet: 0.83 (0.23), residues: 494 loop : -0.91 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 188 TYR 0.022 0.001 TYR a 145 PHE 0.022 0.001 PHE E 324 TRP 0.009 0.001 TRP a 218 HIS 0.003 0.000 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00202 (36559) covalent geometry : angle 0.51508 (49641) hydrogen bonds : bond 0.04160 ( 2166) hydrogen bonds : angle 4.00224 ( 6345) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7582 (t0) cc_final: 0.7277 (t0) REVERT: C 472 LEU cc_start: 0.8757 (tp) cc_final: 0.8556 (tp) REVERT: D 309 TYR cc_start: 0.8379 (t80) cc_final: 0.8145 (t80) REVERT: D 355 ILE cc_start: 0.8967 (tp) cc_final: 0.8680 (tp) REVERT: 1 9 ILE cc_start: 0.2186 (mt) cc_final: 0.1981 (mm) REVERT: 1 21 MET cc_start: 0.7215 (tpp) cc_final: 0.6174 (tpp) REVERT: 1 75 MET cc_start: 0.7683 (ppp) cc_final: 0.7362 (ppp) REVERT: 3 75 MET cc_start: 0.6709 (tmm) cc_final: 0.6121 (tmm) REVERT: 6 39 LEU cc_start: 0.8840 (mt) cc_final: 0.8594 (mt) REVERT: 9 37 ASN cc_start: 0.7713 (t0) cc_final: 0.7215 (t0) REVERT: 9 70 ILE cc_start: 0.8463 (tp) cc_final: 0.8214 (tp) outliers start: 1 outliers final: 0 residues processed: 393 average time/residue: 0.1882 time to fit residues: 128.4838 Evaluate side-chains 275 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 429 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 232 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 450 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 353 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN D 175 ASN F 55 GLN 6 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.065296 restraints weight = 142755.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.065508 restraints weight = 104850.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065360 restraints weight = 86545.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.065761 restraints weight = 73289.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065878 restraints weight = 61786.549| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36559 Z= 0.149 Angle : 0.550 10.142 49641 Z= 0.280 Chirality : 0.041 0.254 5826 Planarity : 0.004 0.045 6454 Dihedral : 6.411 88.637 5333 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.12), residues: 4784 helix: 2.45 (0.10), residues: 2515 sheet: 0.62 (0.22), residues: 512 loop : -0.95 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 195 TYR 0.012 0.001 TYR A 206 PHE 0.020 0.001 PHE 9 74 TRP 0.014 0.001 TRP E 118 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00334 (36559) covalent geometry : angle 0.55006 (49641) hydrogen bonds : bond 0.04704 ( 2166) hydrogen bonds : angle 4.08799 ( 6345) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7731 (t0) cc_final: 0.7450 (t0) REVERT: B 159 MET cc_start: 0.7319 (mmp) cc_final: 0.6879 (mmm) REVERT: G 206 MET cc_start: 0.8583 (mmt) cc_final: 0.8208 (mmt) REVERT: 1 9 ILE cc_start: 0.2464 (mt) cc_final: 0.2168 (mt) REVERT: 1 21 MET cc_start: 0.6826 (tpp) cc_final: 0.6464 (tpp) REVERT: 1 75 MET cc_start: 0.7684 (ppp) cc_final: 0.7400 (ppp) REVERT: 9 37 ASN cc_start: 0.7772 (t0) cc_final: 0.6268 (m110) REVERT: 9 65 GLU cc_start: 0.7353 (mp0) cc_final: 0.6931 (mm-30) REVERT: 9 70 ILE cc_start: 0.8511 (tp) cc_final: 0.8250 (tp) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1827 time to fit residues: 114.1078 Evaluate side-chains 258 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 143 optimal weight: 0.4980 chunk 112 optimal weight: 0.0870 chunk 336 optimal weight: 5.9990 chunk 391 optimal weight: 1.9990 chunk 475 optimal weight: 0.9980 chunk 410 optimal weight: 0.5980 chunk 341 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 478 optimal weight: 3.9990 chunk 462 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN F 291 GLN a 229 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.065970 restraints weight = 142328.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.066649 restraints weight = 98855.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066901 restraints weight = 70398.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067211 restraints weight = 59097.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.067343 restraints weight = 51639.868| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36559 Z= 0.110 Angle : 0.529 10.071 49641 Z= 0.265 Chirality : 0.040 0.248 5826 Planarity : 0.004 0.064 6454 Dihedral : 6.227 83.859 5333 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.12), residues: 4784 helix: 2.52 (0.10), residues: 2512 sheet: 0.74 (0.23), residues: 497 loop : -0.92 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 188 TYR 0.010 0.001 TYR B 281 PHE 0.019 0.001 PHE 8 57 TRP 0.021 0.001 TRP F 118 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00228 (36559) covalent geometry : angle 0.52874 (49641) hydrogen bonds : bond 0.04259 ( 2166) hydrogen bonds : angle 3.97166 ( 6345) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7670 (t0) cc_final: 0.7386 (t0) REVERT: B 159 MET cc_start: 0.7233 (mmp) cc_final: 0.6813 (mmm) REVERT: G 293 ILE cc_start: 0.8256 (tt) cc_final: 0.8054 (tt) REVERT: 1 21 MET cc_start: 0.6783 (tpp) cc_final: 0.5689 (tmm) REVERT: 1 75 MET cc_start: 0.7626 (ppp) cc_final: 0.7342 (ppp) REVERT: 9 37 ASN cc_start: 0.7609 (t0) cc_final: 0.7115 (t0) REVERT: 9 65 GLU cc_start: 0.7047 (mp0) cc_final: 0.6641 (mp0) REVERT: 9 70 ILE cc_start: 0.8512 (tp) cc_final: 0.8227 (tp) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1824 time to fit residues: 114.6378 Evaluate side-chains 264 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 436 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 446 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 460 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 454 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN a 229 GLN d 104 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.083046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066495 restraints weight = 142432.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066942 restraints weight = 100406.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.067070 restraints weight = 83872.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.067585 restraints weight = 65912.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.067891 restraints weight = 54741.183| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36559 Z= 0.106 Angle : 0.528 10.013 49641 Z= 0.263 Chirality : 0.040 0.256 5826 Planarity : 0.004 0.066 6454 Dihedral : 6.087 79.777 5333 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.12), residues: 4784 helix: 2.58 (0.10), residues: 2506 sheet: 0.84 (0.23), residues: 491 loop : -0.88 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 188 TYR 0.012 0.001 TYR B 281 PHE 0.032 0.001 PHE a 221 TRP 0.028 0.001 TRP D 118 HIS 0.004 0.001 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00218 (36559) covalent geometry : angle 0.52844 (49641) hydrogen bonds : bond 0.04068 ( 2166) hydrogen bonds : angle 3.88521 ( 6345) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7634 (t0) cc_final: 0.7330 (t0) REVERT: B 159 MET cc_start: 0.7390 (mmp) cc_final: 0.6959 (mmm) REVERT: D 355 ILE cc_start: 0.8987 (tp) cc_final: 0.8727 (tp) REVERT: 1 21 MET cc_start: 0.6701 (tpp) cc_final: 0.6401 (tpp) REVERT: 1 58 PHE cc_start: 0.7082 (m-10) cc_final: 0.6812 (m-10) REVERT: 1 75 MET cc_start: 0.7645 (ppp) cc_final: 0.7379 (ppp) REVERT: 3 75 MET cc_start: 0.6823 (tmm) cc_final: 0.6222 (tmm) REVERT: 6 39 LEU cc_start: 0.8935 (mt) cc_final: 0.8729 (mt) REVERT: 9 37 ASN cc_start: 0.7543 (t0) cc_final: 0.7087 (t0) REVERT: 9 65 GLU cc_start: 0.7233 (mp0) cc_final: 0.6922 (mm-30) REVERT: 9 70 ILE cc_start: 0.8496 (tp) cc_final: 0.8181 (tp) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1848 time to fit residues: 117.6642 Evaluate side-chains 266 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 340 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 445 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 304 optimal weight: 6.9990 chunk 309 optimal weight: 0.9990 chunk 398 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 416 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN a 229 GLN d 104 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064822 restraints weight = 143043.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064983 restraints weight = 101115.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.065368 restraints weight = 83763.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.065900 restraints weight = 62451.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.066065 restraints weight = 54962.226| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36559 Z= 0.136 Angle : 0.558 10.272 49641 Z= 0.280 Chirality : 0.041 0.274 5826 Planarity : 0.004 0.074 6454 Dihedral : 6.107 79.622 5333 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.12), residues: 4784 helix: 2.53 (0.10), residues: 2509 sheet: 0.70 (0.23), residues: 500 loop : -0.93 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 188 TYR 0.014 0.001 TYR a 145 PHE 0.022 0.001 PHE F 324 TRP 0.024 0.001 TRP D 118 HIS 0.005 0.001 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00305 (36559) covalent geometry : angle 0.55773 (49641) hydrogen bonds : bond 0.04487 ( 2166) hydrogen bonds : angle 4.00890 ( 6345) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7733 (t0) cc_final: 0.7413 (t0) REVERT: B 159 MET cc_start: 0.7439 (mmp) cc_final: 0.7012 (mmm) REVERT: D 355 ILE cc_start: 0.9115 (tp) cc_final: 0.8832 (tp) REVERT: a 83 MET cc_start: 0.7669 (pmm) cc_final: 0.7438 (pmm) REVERT: 1 21 MET cc_start: 0.6673 (tpp) cc_final: 0.6375 (tpp) REVERT: 1 75 MET cc_start: 0.7637 (ppp) cc_final: 0.7383 (ppp) REVERT: 3 75 MET cc_start: 0.6886 (tmm) cc_final: 0.6170 (tmm) REVERT: 9 37 ASN cc_start: 0.7598 (t0) cc_final: 0.7088 (t0) REVERT: 9 65 GLU cc_start: 0.7306 (mp0) cc_final: 0.6848 (mm-30) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1830 time to fit residues: 112.4856 Evaluate side-chains 266 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 83 optimal weight: 0.0980 chunk 374 optimal weight: 2.9990 chunk 430 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 474 optimal weight: 0.6980 chunk 304 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN a 229 GLN d 104 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.066108 restraints weight = 141912.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066389 restraints weight = 101858.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.066490 restraints weight = 71355.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066629 restraints weight = 69471.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.066779 restraints weight = 62814.514| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36559 Z= 0.120 Angle : 0.550 10.231 49641 Z= 0.275 Chirality : 0.040 0.271 5826 Planarity : 0.004 0.065 6454 Dihedral : 6.036 79.954 5333 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.12), residues: 4784 helix: 2.55 (0.10), residues: 2505 sheet: 0.82 (0.23), residues: 487 loop : -0.93 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 188 TYR 0.016 0.001 TYR a 145 PHE 0.044 0.001 PHE 5 80 TRP 0.022 0.001 TRP E 118 HIS 0.004 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00261 (36559) covalent geometry : angle 0.54952 (49641) hydrogen bonds : bond 0.04353 ( 2166) hydrogen bonds : angle 3.96936 ( 6345) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.320 Fit side-chains REVERT: A 173 ASP cc_start: 0.7758 (t0) cc_final: 0.7405 (t0) REVERT: A 229 MET cc_start: 0.8314 (tpp) cc_final: 0.8070 (tpp) REVERT: B 159 MET cc_start: 0.7408 (mmp) cc_final: 0.7004 (mmm) REVERT: D 355 ILE cc_start: 0.9051 (tp) cc_final: 0.8784 (tp) REVERT: a 83 MET cc_start: 0.7590 (pmm) cc_final: 0.7331 (pmm) REVERT: 1 21 MET cc_start: 0.6845 (tpp) cc_final: 0.6494 (tpp) REVERT: 1 58 PHE cc_start: 0.7001 (m-10) cc_final: 0.6759 (m-10) REVERT: 1 75 MET cc_start: 0.7568 (ppp) cc_final: 0.7336 (ppp) REVERT: 3 75 MET cc_start: 0.6813 (tmm) cc_final: 0.6135 (tmm) REVERT: 9 37 ASN cc_start: 0.7649 (t0) cc_final: 0.7163 (t0) REVERT: 9 48 GLU cc_start: 0.8192 (tp30) cc_final: 0.7813 (tm-30) REVERT: 9 65 GLU cc_start: 0.6716 (mp0) cc_final: 0.6448 (mp0) REVERT: 9 70 ILE cc_start: 0.8557 (tp) cc_final: 0.8333 (tp) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1853 time to fit residues: 116.9707 Evaluate side-chains 265 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 387 optimal weight: 0.3980 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 461 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 427 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN a 229 GLN d 104 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.066081 restraints weight = 141829.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.066277 restraints weight = 98897.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.066331 restraints weight = 75598.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066661 restraints weight = 67945.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066739 restraints weight = 60455.314| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36559 Z= 0.124 Angle : 0.566 10.801 49641 Z= 0.282 Chirality : 0.041 0.289 5826 Planarity : 0.004 0.065 6454 Dihedral : 5.972 79.737 5333 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.12), residues: 4784 helix: 2.53 (0.10), residues: 2506 sheet: 0.81 (0.23), residues: 485 loop : -0.94 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 188 TYR 0.015 0.001 TYR a 145 PHE 0.042 0.001 PHE 8 58 TRP 0.021 0.001 TRP E 118 HIS 0.004 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00272 (36559) covalent geometry : angle 0.56588 (49641) hydrogen bonds : bond 0.04389 ( 2166) hydrogen bonds : angle 4.00772 ( 6345) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7757 (t0) cc_final: 0.7410 (t0) REVERT: B 159 MET cc_start: 0.7445 (mmp) cc_final: 0.6996 (mmm) REVERT: D 309 TYR cc_start: 0.8387 (t80) cc_final: 0.8124 (t80) REVERT: D 355 ILE cc_start: 0.9043 (tp) cc_final: 0.8822 (tp) REVERT: 1 21 MET cc_start: 0.6953 (tpp) cc_final: 0.6677 (tpp) REVERT: 1 58 PHE cc_start: 0.7116 (m-10) cc_final: 0.6804 (m-10) REVERT: 1 75 MET cc_start: 0.7551 (ppp) cc_final: 0.7253 (ppp) REVERT: 3 75 MET cc_start: 0.6810 (tmm) cc_final: 0.6160 (tmm) REVERT: 9 37 ASN cc_start: 0.7564 (t0) cc_final: 0.7070 (t0) REVERT: 9 48 GLU cc_start: 0.8261 (tp30) cc_final: 0.7877 (tm-30) REVERT: 9 70 ILE cc_start: 0.8576 (tp) cc_final: 0.8324 (tp) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1866 time to fit residues: 115.6126 Evaluate side-chains 269 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 467 optimal weight: 0.9990 chunk 344 optimal weight: 0.3980 chunk 430 optimal weight: 0.7980 chunk 432 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 201 optimal weight: 0.0270 chunk 368 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 299 optimal weight: 0.6980 chunk 439 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN D 175 ASN F 55 GLN a 229 GLN d 104 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066663 restraints weight = 141187.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067188 restraints weight = 97479.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.067459 restraints weight = 69165.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067713 restraints weight = 61140.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067802 restraints weight = 54299.055| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 36559 Z= 0.110 Angle : 0.554 10.698 49641 Z= 0.275 Chirality : 0.040 0.272 5826 Planarity : 0.004 0.065 6454 Dihedral : 5.848 79.498 5333 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.13), residues: 4784 helix: 2.57 (0.10), residues: 2508 sheet: 0.87 (0.23), residues: 485 loop : -0.88 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 188 TYR 0.015 0.001 TYR a 145 PHE 0.031 0.001 PHE 5 80 TRP 0.019 0.001 TRP E 118 HIS 0.004 0.000 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00227 (36559) covalent geometry : angle 0.55427 (49641) hydrogen bonds : bond 0.04098 ( 2166) hydrogen bonds : angle 3.93703 ( 6345) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8338 (mtp) cc_final: 0.7938 (mpp) REVERT: A 173 ASP cc_start: 0.7642 (t0) cc_final: 0.7398 (t0) REVERT: B 159 MET cc_start: 0.7463 (mmp) cc_final: 0.6978 (mmm) REVERT: D 355 ILE cc_start: 0.9009 (tp) cc_final: 0.8795 (tp) REVERT: G 206 MET cc_start: 0.8444 (mmt) cc_final: 0.8099 (mmt) REVERT: 1 21 MET cc_start: 0.6875 (tpp) cc_final: 0.6486 (tpp) REVERT: 1 58 PHE cc_start: 0.7082 (m-10) cc_final: 0.6769 (m-10) REVERT: 1 75 MET cc_start: 0.7504 (ppp) cc_final: 0.7199 (ppp) REVERT: 9 37 ASN cc_start: 0.7521 (t0) cc_final: 0.7044 (t0) REVERT: 9 48 GLU cc_start: 0.8304 (tp30) cc_final: 0.7893 (tm-30) REVERT: 9 70 ILE cc_start: 0.8555 (tp) cc_final: 0.8296 (tp) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1916 time to fit residues: 120.7570 Evaluate side-chains 266 residues out of total 3768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 251 optimal weight: 4.9990 chunk 277 optimal weight: 0.0570 chunk 27 optimal weight: 0.7980 chunk 290 optimal weight: 0.5980 chunk 303 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 324 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 205 optimal weight: 0.0070 chunk 461 optimal weight: 2.9990 chunk 456 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN a 229 GLN d 104 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.083072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067034 restraints weight = 141209.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067172 restraints weight = 105089.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067238 restraints weight = 78635.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.067471 restraints weight = 71981.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067809 restraints weight = 61121.774| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36559 Z= 0.112 Angle : 0.557 11.150 49641 Z= 0.276 Chirality : 0.040 0.277 5826 Planarity : 0.004 0.064 6454 Dihedral : 5.781 78.401 5333 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.59 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.13), residues: 4784 helix: 2.59 (0.10), residues: 2508 sheet: 0.89 (0.23), residues: 485 loop : -0.87 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 188 TYR 0.016 0.001 TYR a 145 PHE 0.030 0.001 PHE 5 80 TRP 0.019 0.001 TRP E 118 HIS 0.006 0.001 HIS F 326 Details of bonding type rmsd covalent geometry : bond 0.00238 (36559) covalent geometry : angle 0.55710 (49641) hydrogen bonds : bond 0.04087 ( 2166) hydrogen bonds : angle 3.93322 ( 6345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4723.37 seconds wall clock time: 82 minutes 47.81 seconds (4967.81 seconds total)