Starting phenix.real_space_refine on Mon Jan 13 17:13:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xoo_38536/01_2025/8xoo_38536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xoo_38536/01_2025/8xoo_38536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xoo_38536/01_2025/8xoo_38536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xoo_38536/01_2025/8xoo_38536.map" model { file = "/net/cci-nas-00/data/ceres_data/8xoo_38536/01_2025/8xoo_38536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xoo_38536/01_2025/8xoo_38536.cif" } resolution = 1.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 sd= 1.301 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 31 5.49 5 Mg 7 5.21 5 S 161 5.16 5 C 29558 2.51 5 N 8270 2.21 5 O 9202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 47229 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "B" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "C" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "D" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "E" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1369 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "H" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1371 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain: "I" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1399 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "J" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1355 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain: "K" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "L" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "M" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1355 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain: "N" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1355 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain: "R" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4636 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 22, 'TRANS': 569} Chain breaks: 1 Chain: "Q" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4636 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 22, 'TRANS': 569} Chain breaks: 1 Chain: "P" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4636 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 22, 'TRANS': 569} Chain breaks: 1 Chain: "O" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4486 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 22, 'TRANS': 549} Chain breaks: 2 Chain: "T" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4632 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 569} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4609 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 22, 'TRANS': 564} Chain breaks: 2 Chain: "X" Number of atoms: 125 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 113 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AUNK X 4 " occ=0.77 ... (8 atoms not shown) pdb=" CB BUNK X 4 " occ=0.23 Time building chain proxies: 20.47, per 1000 atoms: 0.43 Number of scatterers: 47229 At special positions: 0 Unit cell: (151.2, 136.92, 212.52, 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 161 16.00 P 31 15.00 Mg 7 11.99 O 9202 8.00 N 8270 7.00 C 29558 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.13 Conformation dependent library (CDL) restraints added in 4.6 seconds 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11210 Finding SS restraints... Secondary structure from input PDB file: 290 helices and 68 sheets defined 56.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 removed outlier: 4.244A pdb=" N GLN A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.919A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.503A pdb=" N GLY B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 removed outlier: 3.792A pdb=" N PHE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 174 Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.930A pdb=" N ILE B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 199 Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 85 through 99 Processing helix chain 'C' and resid 113 through 121 removed outlier: 3.567A pdb=" N PHE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 173 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 113 through 121 removed outlier: 3.546A pdb=" N PHE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 174 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 191 through 199 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.555A pdb=" N ILE E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 removed outlier: 3.604A pdb=" N PHE E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 174 Processing helix chain 'E' and resid 176 through 186 removed outlier: 4.637A pdb=" N ARG E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 85 through 99 removed outlier: 3.532A pdb=" N ILE F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 148 through 174 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 191 through 199 Processing helix chain 'G' and resid 32 through 44 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 85 through 99 Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 148 through 174 Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'H' and resid 53 through 60 Processing helix chain 'H' and resid 70 through 88 Processing helix chain 'H' and resid 103 through 117 Processing helix chain 'H' and resid 131 through 139 Processing helix chain 'H' and resid 167 through 191 removed outlier: 3.557A pdb=" N HIS H 191 " --> pdb=" O MET H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 203 Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 53 through 60 Processing helix chain 'I' and resid 70 through 88 Processing helix chain 'I' and resid 103 through 117 removed outlier: 3.591A pdb=" N LEU I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 139 Processing helix chain 'I' and resid 167 through 191 Processing helix chain 'I' and resid 195 through 203 Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 70 through 88 Processing helix chain 'J' and resid 103 through 117 removed outlier: 3.708A pdb=" N VAL J 117 " --> pdb=" O THR J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 139 Processing helix chain 'J' and resid 166 through 191 Processing helix chain 'J' and resid 195 through 203 Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'K' and resid 53 through 60 Processing helix chain 'K' and resid 70 through 88 Processing helix chain 'K' and resid 103 through 117 removed outlier: 3.728A pdb=" N VAL K 117 " --> pdb=" O THR K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 139 removed outlier: 3.506A pdb=" N VAL K 135 " --> pdb=" O ALA K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 191 Processing helix chain 'K' and resid 195 through 203 Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 53 through 61 Processing helix chain 'L' and resid 70 through 88 Processing helix chain 'L' and resid 103 through 117 Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 167 through 191 removed outlier: 3.511A pdb=" N HIS L 191 " --> pdb=" O MET L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 203 Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'M' and resid 53 through 60 Processing helix chain 'M' and resid 70 through 88 Processing helix chain 'M' and resid 104 through 117 Processing helix chain 'M' and resid 131 through 139 removed outlier: 3.726A pdb=" N VAL M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU M 136 " --> pdb=" O ALA M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 191 Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 210 through 217 Processing helix chain 'N' and resid 53 through 60 Processing helix chain 'N' and resid 70 through 88 Processing helix chain 'N' and resid 103 through 117 Processing helix chain 'N' and resid 131 through 139 Processing helix chain 'N' and resid 167 through 191 Processing helix chain 'N' and resid 195 through 203 Processing helix chain 'N' and resid 211 through 218 Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.572A pdb=" N GLU R 180 " --> pdb=" O GLN R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 201 Processing helix chain 'R' and resid 217 through 232 removed outlier: 3.859A pdb=" N VAL R 222 " --> pdb=" O LYS R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 255 removed outlier: 4.418A pdb=" N GLY R 254 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 276 Processing helix chain 'R' and resid 299 through 310 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 331 through 337 Processing helix chain 'R' and resid 347 through 367 removed outlier: 4.906A pdb=" N ASP R 360 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG R 361 " --> pdb=" O GLY R 357 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 386 Processing helix chain 'R' and resid 390 through 410 removed outlier: 3.565A pdb=" N ALA R 395 " --> pdb=" O LEU R 391 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE R 396 " --> pdb=" O PRO R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 476 through 489 Processing helix chain 'R' and resid 496 through 505 Processing helix chain 'R' and resid 505 through 511 Processing helix chain 'R' and resid 517 through 533 removed outlier: 3.667A pdb=" N VAL R 521 " --> pdb=" O GLN R 517 " (cutoff:3.500A) Processing helix chain 'R' and resid 554 through 568 removed outlier: 3.555A pdb=" N SER R 559 " --> pdb=" O LYS R 555 " (cutoff:3.500A) Processing helix chain 'R' and resid 569 through 573 removed outlier: 3.705A pdb=" N LEU R 573 " --> pdb=" O GLU R 570 " (cutoff:3.500A) Processing helix chain 'R' and resid 579 through 582 removed outlier: 3.972A pdb=" N SER R 582 " --> pdb=" O SER R 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 579 through 582' Processing helix chain 'R' and resid 583 through 586 Processing helix chain 'R' and resid 587 through 592 removed outlier: 3.608A pdb=" N PHE R 591 " --> pdb=" O VAL R 587 " (cutoff:3.500A) Processing helix chain 'R' and resid 604 through 613 removed outlier: 3.873A pdb=" N LYS R 609 " --> pdb=" O GLN R 605 " (cutoff:3.500A) Processing helix chain 'R' and resid 622 through 626 Processing helix chain 'R' and resid 630 through 640 removed outlier: 3.688A pdb=" N LEU R 634 " --> pdb=" O ILE R 630 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN R 636 " --> pdb=" O ASN R 632 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE R 637 " --> pdb=" O SER R 633 " (cutoff:3.500A) Processing helix chain 'R' and resid 682 through 702 removed outlier: 3.520A pdb=" N TYR R 687 " --> pdb=" O THR R 683 " (cutoff:3.500A) Processing helix chain 'R' and resid 703 through 709 removed outlier: 3.912A pdb=" N ARG R 709 " --> pdb=" O GLU R 705 " (cutoff:3.500A) Processing helix chain 'R' and resid 720 through 740 removed outlier: 3.831A pdb=" N ASP R 729 " --> pdb=" O LEU R 725 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU R 730 " --> pdb=" O LYS R 726 " (cutoff:3.500A) Processing helix chain 'R' and resid 749 through 759 Processing helix chain 'R' and resid 767 through 778 Processing helix chain 'R' and resid 778 through 789 Processing helix chain 'Q' and resid 165 through 170 Processing helix chain 'Q' and resid 174 through 180 Processing helix chain 'Q' and resid 189 through 201 Processing helix chain 'Q' and resid 217 through 231 removed outlier: 3.667A pdb=" N VAL Q 222 " --> pdb=" O LYS Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 260 through 275 Processing helix chain 'Q' and resid 285 through 289 Processing helix chain 'Q' and resid 299 through 311 Proline residue: Q 306 - end of helix Processing helix chain 'Q' and resid 320 through 327 Processing helix chain 'Q' and resid 331 through 336 Processing helix chain 'Q' and resid 347 through 367 removed outlier: 4.517A pdb=" N ASP Q 360 " --> pdb=" O LYS Q 356 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG Q 361 " --> pdb=" O GLY Q 357 " (cutoff:3.500A) Processing helix chain 'Q' and resid 371 through 386 removed outlier: 3.595A pdb=" N ILE Q 386 " --> pdb=" O ALA Q 382 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 410 removed outlier: 3.521A pdb=" N ARG Q 410 " --> pdb=" O MET Q 406 " (cutoff:3.500A) Processing helix chain 'Q' and resid 476 through 489 Processing helix chain 'Q' and resid 496 through 505 Processing helix chain 'Q' and resid 505 through 511 Processing helix chain 'Q' and resid 517 through 534 removed outlier: 3.558A pdb=" N GLY Q 534 " --> pdb=" O ARG Q 530 " (cutoff:3.500A) Processing helix chain 'Q' and resid 554 through 567 removed outlier: 3.548A pdb=" N SER Q 559 " --> pdb=" O LYS Q 555 " (cutoff:3.500A) Processing helix chain 'Q' and resid 569 through 573 removed outlier: 3.690A pdb=" N ALA Q 572 " --> pdb=" O ASP Q 569 " (cutoff:3.500A) Processing helix chain 'Q' and resid 579 through 581 No H-bonds generated for 'chain 'Q' and resid 579 through 581' Processing helix chain 'Q' and resid 583 through 586 Processing helix chain 'Q' and resid 587 through 592 removed outlier: 3.603A pdb=" N PHE Q 591 " --> pdb=" O VAL Q 587 " (cutoff:3.500A) Processing helix chain 'Q' and resid 605 through 612 Processing helix chain 'Q' and resid 622 through 626 Processing helix chain 'Q' and resid 629 through 633 Processing helix chain 'Q' and resid 634 through 640 Processing helix chain 'Q' and resid 685 through 702 Processing helix chain 'Q' and resid 703 through 708 Processing helix chain 'Q' and resid 720 through 741 removed outlier: 3.854A pdb=" N ASP Q 729 " --> pdb=" O LEU Q 725 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU Q 730 " --> pdb=" O LYS Q 726 " (cutoff:3.500A) Processing helix chain 'Q' and resid 749 through 760 Processing helix chain 'Q' and resid 767 through 789 removed outlier: 4.477A pdb=" N ASP Q 780 " --> pdb=" O ARG Q 776 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER Q 781 " --> pdb=" O GLU Q 777 " (cutoff:3.500A) Processing helix chain 'Q' and resid 804 through 808 removed outlier: 3.705A pdb=" N LYS Q 808 " --> pdb=" O GLY Q 805 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 170 removed outlier: 3.571A pdb=" N PHE P 170 " --> pdb=" O VAL P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 180 Processing helix chain 'P' and resid 189 through 201 Processing helix chain 'P' and resid 217 through 231 removed outlier: 3.777A pdb=" N VAL P 222 " --> pdb=" O LYS P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 253 removed outlier: 3.728A pdb=" N LEU P 251 " --> pdb=" O ASP P 247 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 276 Processing helix chain 'P' and resid 285 through 289 removed outlier: 3.849A pdb=" N VAL P 289 " --> pdb=" O HIS P 286 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 311 Proline residue: P 306 - end of helix Processing helix chain 'P' and resid 320 through 327 Processing helix chain 'P' and resid 328 through 330 No H-bonds generated for 'chain 'P' and resid 328 through 330' Processing helix chain 'P' and resid 331 through 337 removed outlier: 3.941A pdb=" N ARG P 337 " --> pdb=" O ALA P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 347 through 367 removed outlier: 4.494A pdb=" N ASP P 360 " --> pdb=" O LYS P 356 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG P 361 " --> pdb=" O GLY P 357 " (cutoff:3.500A) Processing helix chain 'P' and resid 371 through 385 Processing helix chain 'P' and resid 390 through 409 removed outlier: 3.683A pdb=" N ILE P 396 " --> pdb=" O PRO P 392 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU P 398 " --> pdb=" O LYS P 394 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE P 399 " --> pdb=" O ALA P 395 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG P 409 " --> pdb=" O ARG P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 476 through 489 Processing helix chain 'P' and resid 496 through 505 Processing helix chain 'P' and resid 505 through 512 Processing helix chain 'P' and resid 517 through 533 Processing helix chain 'P' and resid 554 through 568 Processing helix chain 'P' and resid 569 through 573 removed outlier: 3.536A pdb=" N ALA P 572 " --> pdb=" O ASP P 569 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU P 573 " --> pdb=" O GLU P 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 569 through 573' Processing helix chain 'P' and resid 583 through 586 Processing helix chain 'P' and resid 587 through 592 removed outlier: 3.934A pdb=" N PHE P 591 " --> pdb=" O VAL P 587 " (cutoff:3.500A) Processing helix chain 'P' and resid 605 through 613 Processing helix chain 'P' and resid 622 through 626 Processing helix chain 'P' and resid 627 through 633 removed outlier: 3.522A pdb=" N ASN P 632 " --> pdb=" O ASP P 629 " (cutoff:3.500A) Processing helix chain 'P' and resid 634 through 641 Processing helix chain 'P' and resid 685 through 702 Processing helix chain 'P' and resid 703 through 708 Processing helix chain 'P' and resid 720 through 740 removed outlier: 3.713A pdb=" N ILE P 724 " --> pdb=" O SER P 720 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU P 725 " --> pdb=" O GLN P 721 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS P 726 " --> pdb=" O ALA P 722 " (cutoff:3.500A) Processing helix chain 'P' and resid 741 through 743 No H-bonds generated for 'chain 'P' and resid 741 through 743' Processing helix chain 'P' and resid 749 through 760 Processing helix chain 'P' and resid 767 through 778 Processing helix chain 'P' and resid 778 through 789 Processing helix chain 'P' and resid 804 through 808 Processing helix chain 'O' and resid 165 through 170 Processing helix chain 'O' and resid 174 through 180 Processing helix chain 'O' and resid 189 through 201 Processing helix chain 'O' and resid 217 through 231 removed outlier: 3.862A pdb=" N VAL O 222 " --> pdb=" O LYS O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 253 removed outlier: 3.515A pdb=" N LEU O 251 " --> pdb=" O ASP O 247 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 276 removed outlier: 3.736A pdb=" N ARG O 264 " --> pdb=" O ASP O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 310 removed outlier: 3.536A pdb=" N ILE O 303 " --> pdb=" O ASP O 299 " (cutoff:3.500A) Proline residue: O 306 - end of helix Processing helix chain 'O' and resid 320 through 328 Processing helix chain 'O' and resid 331 through 337 removed outlier: 4.076A pdb=" N ARG O 337 " --> pdb=" O ALA O 333 " (cutoff:3.500A) Processing helix chain 'O' and resid 347 through 366 removed outlier: 4.680A pdb=" N ASP O 360 " --> pdb=" O LYS O 356 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ARG O 361 " --> pdb=" O GLY O 357 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR O 362 " --> pdb=" O LEU O 358 " (cutoff:3.500A) Processing helix chain 'O' and resid 371 through 386 Processing helix chain 'O' and resid 390 through 410 removed outlier: 3.592A pdb=" N ALA O 395 " --> pdb=" O LEU O 391 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE O 396 " --> pdb=" O PRO O 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 476 through 488 Processing helix chain 'O' and resid 496 through 505 Processing helix chain 'O' and resid 505 through 514 removed outlier: 3.586A pdb=" N ARG O 513 " --> pdb=" O GLU O 509 " (cutoff:3.500A) Processing helix chain 'O' and resid 519 through 533 Processing helix chain 'O' and resid 554 through 568 Processing helix chain 'O' and resid 569 through 571 No H-bonds generated for 'chain 'O' and resid 569 through 571' Processing helix chain 'O' and resid 579 through 581 No H-bonds generated for 'chain 'O' and resid 579 through 581' Processing helix chain 'O' and resid 583 through 586 Processing helix chain 'O' and resid 587 through 592 removed outlier: 3.625A pdb=" N PHE O 591 " --> pdb=" O VAL O 587 " (cutoff:3.500A) Processing helix chain 'O' and resid 604 through 613 Processing helix chain 'O' and resid 622 through 626 Processing helix chain 'O' and resid 627 through 628 No H-bonds generated for 'chain 'O' and resid 627 through 628' Processing helix chain 'O' and resid 629 through 640 removed outlier: 4.044A pdb=" N SER O 633 " --> pdb=" O ASP O 629 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN O 636 " --> pdb=" O ASN O 632 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE O 637 " --> pdb=" O SER O 633 " (cutoff:3.500A) Processing helix chain 'O' and resid 689 through 702 removed outlier: 3.573A pdb=" N SER O 695 " --> pdb=" O LYS O 691 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP O 696 " --> pdb=" O ASN O 692 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU O 697 " --> pdb=" O LYS O 693 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS O 699 " --> pdb=" O SER O 695 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN O 700 " --> pdb=" O ASP O 696 " (cutoff:3.500A) Processing helix chain 'O' and resid 703 through 708 Processing helix chain 'O' and resid 720 through 740 Processing helix chain 'O' and resid 749 through 760 Processing helix chain 'O' and resid 767 through 769 No H-bonds generated for 'chain 'O' and resid 767 through 769' Processing helix chain 'O' and resid 770 through 778 Processing helix chain 'O' and resid 778 through 788 removed outlier: 3.502A pdb=" N LEU O 782 " --> pdb=" O ILE O 778 " (cutoff:3.500A) Processing helix chain 'O' and resid 804 through 808 removed outlier: 4.117A pdb=" N THR O 807 " --> pdb=" O GLU O 804 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS O 808 " --> pdb=" O GLY O 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 804 through 808' Processing helix chain 'T' and resid 165 through 170 Processing helix chain 'T' and resid 174 through 180 Processing helix chain 'T' and resid 189 through 201 Processing helix chain 'T' and resid 217 through 232 Processing helix chain 'T' and resid 247 through 253 removed outlier: 4.141A pdb=" N LEU T 251 " --> pdb=" O ASP T 247 " (cutoff:3.500A) Processing helix chain 'T' and resid 257 through 276 removed outlier: 3.616A pdb=" N PHE T 261 " --> pdb=" O TYR T 257 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU T 263 " --> pdb=" O GLY T 259 " (cutoff:3.500A) Processing helix chain 'T' and resid 284 through 290 removed outlier: 3.676A pdb=" N LEU T 288 " --> pdb=" O ALA T 284 " (cutoff:3.500A) Processing helix chain 'T' and resid 305 through 311 Processing helix chain 'T' and resid 320 through 327 Processing helix chain 'T' and resid 333 through 336 removed outlier: 3.780A pdb=" N ARG T 336 " --> pdb=" O ALA T 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 333 through 336' Processing helix chain 'T' and resid 347 through 367 removed outlier: 4.304A pdb=" N ASP T 360 " --> pdb=" O LYS T 356 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG T 361 " --> pdb=" O GLY T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 371 through 385 Processing helix chain 'T' and resid 390 through 410 removed outlier: 3.533A pdb=" N LYS T 394 " --> pdb=" O PHE T 390 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA T 395 " --> pdb=" O LEU T 391 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE T 396 " --> pdb=" O PRO T 392 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 483 Processing helix chain 'T' and resid 484 through 488 Processing helix chain 'T' and resid 499 through 505 Processing helix chain 'T' and resid 505 through 512 removed outlier: 4.140A pdb=" N GLU T 509 " --> pdb=" O ARG T 505 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 532 Processing helix chain 'T' and resid 555 through 568 Processing helix chain 'T' and resid 579 through 582 removed outlier: 3.665A pdb=" N SER T 582 " --> pdb=" O SER T 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 579 through 582' Processing helix chain 'T' and resid 583 through 591 removed outlier: 3.601A pdb=" N THR T 586 " --> pdb=" O GLU T 583 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER T 588 " --> pdb=" O HIS T 585 " (cutoff:3.500A) Processing helix chain 'T' and resid 604 through 613 removed outlier: 3.720A pdb=" N GLU T 608 " --> pdb=" O GLY T 604 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS T 609 " --> pdb=" O GLN T 605 " (cutoff:3.500A) Processing helix chain 'T' and resid 623 through 626 Processing helix chain 'T' and resid 627 through 641 removed outlier: 3.636A pdb=" N PHE T 631 " --> pdb=" O HIS T 627 " (cutoff:3.500A) Processing helix chain 'T' and resid 683 through 702 Processing helix chain 'T' and resid 703 through 709 Processing helix chain 'T' and resid 720 through 722 No H-bonds generated for 'chain 'T' and resid 720 through 722' Processing helix chain 'T' and resid 723 through 742 removed outlier: 4.133A pdb=" N ILE T 727 " --> pdb=" O ASP T 723 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP T 741 " --> pdb=" O GLU T 737 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG T 742 " --> pdb=" O ARG T 738 " (cutoff:3.500A) Processing helix chain 'T' and resid 749 through 760 Processing helix chain 'T' and resid 767 through 778 Processing helix chain 'T' and resid 778 through 789 removed outlier: 3.615A pdb=" N PHE T 788 " --> pdb=" O GLU T 784 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 170 Processing helix chain 'S' and resid 174 through 180 Processing helix chain 'S' and resid 189 through 201 removed outlier: 4.236A pdb=" N ILE S 193 " --> pdb=" O ARG S 189 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER S 201 " --> pdb=" O MET S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 217 through 232 Processing helix chain 'S' and resid 247 through 253 Processing helix chain 'S' and resid 262 through 276 removed outlier: 3.680A pdb=" N GLY S 276 " --> pdb=" O ILE S 272 " (cutoff:3.500A) Processing helix chain 'S' and resid 284 through 288 Processing helix chain 'S' and resid 300 through 311 removed outlier: 3.785A pdb=" N LEU S 304 " --> pdb=" O ALA S 300 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS S 305 " --> pdb=" O ALA S 301 " (cutoff:3.500A) Proline residue: S 306 - end of helix Processing helix chain 'S' and resid 320 through 327 Processing helix chain 'S' and resid 331 through 336 removed outlier: 4.386A pdb=" N ARG S 336 " --> pdb=" O ALA S 332 " (cutoff:3.500A) Processing helix chain 'S' and resid 347 through 367 removed outlier: 4.482A pdb=" N ASP S 360 " --> pdb=" O LYS S 356 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG S 361 " --> pdb=" O GLY S 357 " (cutoff:3.500A) Processing helix chain 'S' and resid 371 through 386 Processing helix chain 'S' and resid 390 through 409 removed outlier: 3.622A pdb=" N ALA S 395 " --> pdb=" O LEU S 391 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE S 396 " --> pdb=" O PRO S 392 " (cutoff:3.500A) Processing helix chain 'S' and resid 476 through 488 Processing helix chain 'S' and resid 497 through 505 Processing helix chain 'S' and resid 505 through 511 Processing helix chain 'S' and resid 517 through 533 Processing helix chain 'S' and resid 554 through 568 removed outlier: 3.667A pdb=" N SER S 559 " --> pdb=" O LYS S 555 " (cutoff:3.500A) Processing helix chain 'S' and resid 569 through 571 No H-bonds generated for 'chain 'S' and resid 569 through 571' Processing helix chain 'S' and resid 579 through 581 No H-bonds generated for 'chain 'S' and resid 579 through 581' Processing helix chain 'S' and resid 583 through 586 Processing helix chain 'S' and resid 587 through 592 removed outlier: 3.851A pdb=" N PHE S 591 " --> pdb=" O VAL S 587 " (cutoff:3.500A) Processing helix chain 'S' and resid 606 through 613 Processing helix chain 'S' and resid 622 through 626 removed outlier: 3.554A pdb=" N ALA S 626 " --> pdb=" O VAL S 623 " (cutoff:3.500A) Processing helix chain 'S' and resid 627 through 641 removed outlier: 3.776A pdb=" N PHE S 631 " --> pdb=" O HIS S 627 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN S 636 " --> pdb=" O ASN S 632 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE S 637 " --> pdb=" O SER S 633 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU S 638 " --> pdb=" O LEU S 634 " (cutoff:3.500A) Processing helix chain 'S' and resid 666 through 671 removed outlier: 3.537A pdb=" N LYS S 671 " --> pdb=" O ARG S 667 " (cutoff:3.500A) Processing helix chain 'S' and resid 686 through 702 Processing helix chain 'S' and resid 703 through 710 Processing helix chain 'S' and resid 721 through 741 removed outlier: 3.513A pdb=" N LEU S 725 " --> pdb=" O GLN S 721 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS S 726 " --> pdb=" O ALA S 722 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP S 729 " --> pdb=" O LEU S 725 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU S 730 " --> pdb=" O LYS S 726 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP S 741 " --> pdb=" O GLU S 737 " (cutoff:3.500A) Processing helix chain 'S' and resid 749 through 760 Processing helix chain 'S' and resid 767 through 778 Processing helix chain 'S' and resid 782 through 789 Processing helix chain 'S' and resid 804 through 808 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.234A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE A 128 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR A 105 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.234A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A 134 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLY A 109 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU A 136 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 111 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 147 removed outlier: 4.906A pdb=" N LEU A 144 " --> pdb=" O GLY I 163 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLY I 163 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLY A 146 " --> pdb=" O GLU I 161 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU I 161 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.592A pdb=" N ILE B 46 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN B 80 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU B 48 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.592A pdb=" N ILE B 46 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASN B 80 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU B 48 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N PHE B 128 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR B 105 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 48 removed outlier: 4.058A pdb=" N LEU C 48 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE C 128 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR C 105 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 129 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.714A pdb=" N ALA C 111 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB1, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.551A pdb=" N SER K 160 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 48 removed outlier: 3.866A pdb=" N ASN D 80 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER D 81 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 110 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE D 128 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR D 105 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 48 removed outlier: 3.866A pdb=" N ASN D 80 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER D 81 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 110 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLU D 134 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY D 109 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU D 136 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA D 111 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.930A pdb=" N ILE E 46 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASN E 80 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU E 48 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER E 81 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU E 110 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU E 134 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLY E 109 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU E 136 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA E 111 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.930A pdb=" N ILE E 46 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASN E 80 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU E 48 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER E 81 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU E 110 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE E 128 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR E 105 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB9, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.630A pdb=" N SER M 160 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 45 through 49 removed outlier: 3.621A pdb=" N ASN F 80 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE F 128 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR F 105 " --> pdb=" O PHE F 128 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU F 130 " --> pdb=" O THR F 105 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA F 107 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN F 132 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY F 109 " --> pdb=" O ASN F 132 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 129 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 135 through 137 Processing sheet with id=AC3, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AC4, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AC5, first strand: chain 'G' and resid 45 through 48 removed outlier: 5.557A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 134 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 45 through 48 removed outlier: 5.557A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE G 128 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N THR G 105 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 129 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AC8, first strand: chain 'G' and resid 145 through 147 removed outlier: 3.755A pdb=" N GLY G 146 " --> pdb=" O SER H 160 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 160 " --> pdb=" O GLY G 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.493A pdb=" N ILE H 63 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N MET H 146 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR H 123 " --> pdb=" O MET H 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 128 through 130 removed outlier: 6.436A pdb=" N ALA H 129 " --> pdb=" O LEU H 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 62 through 65 Processing sheet with id=AD3, first strand: chain 'I' and resid 128 through 129 removed outlier: 6.290A pdb=" N ALA I 129 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.632A pdb=" N ILE J 63 " --> pdb=" O TYR J 96 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N MET J 146 " --> pdb=" O VAL J 121 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N THR J 123 " --> pdb=" O MET J 146 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN J 222 " --> pdb=" O ARG J 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA J 147 " --> pdb=" O GLN J 222 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 128 through 130 Processing sheet with id=AD6, first strand: chain 'K' and resid 62 through 65 removed outlier: 6.467A pdb=" N ILE K 63 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE K 93 " --> pdb=" O GLN K 122 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL K 124 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL K 95 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET K 146 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR K 123 " --> pdb=" O MET K 146 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN K 222 " --> pdb=" O ARG K 145 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA K 147 " --> pdb=" O GLN K 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'K' and resid 128 through 130 Processing sheet with id=AD8, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.879A pdb=" N ILE L 63 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE L 93 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N MET L 146 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR L 123 " --> pdb=" O MET L 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 128 through 130 removed outlier: 6.406A pdb=" N ALA L 129 " --> pdb=" O LEU L 154 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 62 through 65 removed outlier: 7.962A pdb=" N MET M 146 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR M 123 " --> pdb=" O MET M 146 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN M 222 " --> pdb=" O ARG M 145 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA M 147 " --> pdb=" O GLN M 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 128 through 130 Processing sheet with id=AE3, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.394A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N MET N 146 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR N 123 " --> pdb=" O MET N 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 128 through 130 removed outlier: 6.286A pdb=" N ALA N 129 " --> pdb=" O LEU N 154 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 171 through 173 removed outlier: 5.872A pdb=" N HIS R 242 " --> pdb=" O ILE R 279 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE R 281 " --> pdb=" O HIS R 242 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR R 244 " --> pdb=" O PHE R 281 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR R 319 " --> pdb=" O PRO R 208 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU R 210 " --> pdb=" O THR R 319 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 369 through 370 removed outlier: 6.865A pdb=" N SER R 369 " --> pdb=" O VAL R 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'R' and resid 574 through 577 removed outlier: 6.483A pdb=" N ILE R 574 " --> pdb=" O LEU R 619 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP R 621 " --> pdb=" O ILE R 574 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU R 576 " --> pdb=" O ASP R 621 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL R 618 " --> pdb=" O ILE R 659 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR R 661 " --> pdb=" O VAL R 618 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE R 620 " --> pdb=" O THR R 661 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER R 544 " --> pdb=" O ASP R 712 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL R 714 " --> pdb=" O SER R 544 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE R 546 " --> pdb=" O VAL R 714 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 642 through 644 Processing sheet with id=AE9, first strand: chain 'R' and resid 744 through 746 removed outlier: 6.741A pdb=" N GLY R 745 " --> pdb=" O VAL R 797 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL R 799 " --> pdb=" O GLY R 745 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 171 through 173 removed outlier: 6.474A pdb=" N HIS Q 242 " --> pdb=" O ILE Q 279 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE Q 281 " --> pdb=" O HIS Q 242 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR Q 244 " --> pdb=" O PHE Q 281 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASP Q 283 " --> pdb=" O TYR Q 244 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU Q 246 " --> pdb=" O ASP Q 283 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA Q 318 " --> pdb=" O ILE Q 282 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL Q 209 " --> pdb=" O ILE Q 341 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 369 through 370 removed outlier: 6.594A pdb=" N SER Q 369 " --> pdb=" O VAL Q 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'Q' and resid 574 through 577 removed outlier: 6.649A pdb=" N ILE Q 574 " --> pdb=" O LEU Q 619 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP Q 621 " --> pdb=" O ILE Q 574 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU Q 576 " --> pdb=" O ASP Q 621 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY Q 543 " --> pdb=" O ILE Q 658 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N MET Q 660 " --> pdb=" O GLY Q 543 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE Q 545 " --> pdb=" O MET Q 660 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR Q 662 " --> pdb=" O PHE Q 545 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE Q 547 " --> pdb=" O THR Q 662 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER Q 544 " --> pdb=" O ASP Q 712 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL Q 714 " --> pdb=" O SER Q 544 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE Q 546 " --> pdb=" O VAL Q 714 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 642 through 644 Processing sheet with id=AF5, first strand: chain 'Q' and resid 746 through 748 removed outlier: 6.720A pdb=" N GLU Q 747 " --> pdb=" O VAL Q 799 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N THR Q 801 " --> pdb=" O GLU Q 747 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 171 through 173 removed outlier: 6.480A pdb=" N HIS P 242 " --> pdb=" O ILE P 279 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE P 281 " --> pdb=" O HIS P 242 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR P 244 " --> pdb=" O PHE P 281 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP P 283 " --> pdb=" O TYR P 244 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU P 246 " --> pdb=" O ASP P 283 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA P 318 " --> pdb=" O ILE P 282 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR P 319 " --> pdb=" O PRO P 208 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU P 210 " --> pdb=" O THR P 319 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL P 209 " --> pdb=" O ILE P 341 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 574 through 577 removed outlier: 6.224A pdb=" N GLY P 543 " --> pdb=" O ILE P 658 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N MET P 660 " --> pdb=" O GLY P 543 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE P 545 " --> pdb=" O MET P 660 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N THR P 662 " --> pdb=" O PHE P 545 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE P 547 " --> pdb=" O THR P 662 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 642 through 644 Processing sheet with id=AF9, first strand: chain 'P' and resid 746 through 748 removed outlier: 6.665A pdb=" N GLU P 747 " --> pdb=" O VAL P 799 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N THR P 801 " --> pdb=" O GLU P 747 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 171 through 173 removed outlier: 6.163A pdb=" N HIS O 242 " --> pdb=" O ILE O 279 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE O 281 " --> pdb=" O HIS O 242 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR O 244 " --> pdb=" O PHE O 281 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA O 318 " --> pdb=" O ILE O 282 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N THR O 319 " --> pdb=" O PRO O 208 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU O 210 " --> pdb=" O THR O 319 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 369 through 370 removed outlier: 6.776A pdb=" N SER O 369 " --> pdb=" O VAL O 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'O' and resid 573 through 577 removed outlier: 6.381A pdb=" N ILE O 574 " --> pdb=" O LEU O 619 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASP O 621 " --> pdb=" O ILE O 574 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU O 576 " --> pdb=" O ASP O 621 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL O 618 " --> pdb=" O ILE O 659 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR O 661 " --> pdb=" O VAL O 618 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE O 620 " --> pdb=" O THR O 661 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE O 545 " --> pdb=" O MET O 660 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR O 662 " --> pdb=" O PHE O 545 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE O 547 " --> pdb=" O THR O 662 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL O 714 " --> pdb=" O SER O 544 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE O 546 " --> pdb=" O VAL O 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'O' and resid 642 through 644 Processing sheet with id=AG5, first strand: chain 'O' and resid 746 through 747 removed outlier: 3.606A pdb=" N GLU O 802 " --> pdb=" O THR O 809 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 171 through 173 removed outlier: 4.461A pdb=" N GLN T 314 " --> pdb=" O ILE T 278 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA T 318 " --> pdb=" O ILE T 282 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR T 319 " --> pdb=" O PRO T 208 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU T 210 " --> pdb=" O THR T 319 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 573 through 577 removed outlier: 6.312A pdb=" N ILE T 574 " --> pdb=" O LEU T 619 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASP T 621 " --> pdb=" O ILE T 574 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU T 576 " --> pdb=" O ASP T 621 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL T 618 " --> pdb=" O ILE T 659 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR T 661 " --> pdb=" O VAL T 618 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE T 620 " --> pdb=" O THR T 661 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY T 543 " --> pdb=" O ILE T 658 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N MET T 660 " --> pdb=" O GLY T 543 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE T 545 " --> pdb=" O MET T 660 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR T 662 " --> pdb=" O PHE T 545 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE T 547 " --> pdb=" O THR T 662 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER T 544 " --> pdb=" O ASP T 712 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL T 714 " --> pdb=" O SER T 544 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE T 546 " --> pdb=" O VAL T 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'T' and resid 642 through 644 Processing sheet with id=AG9, first strand: chain 'T' and resid 746 through 748 Processing sheet with id=AH1, first strand: chain 'S' and resid 172 through 173 removed outlier: 6.044A pdb=" N HIS S 242 " --> pdb=" O ILE S 279 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE S 281 " --> pdb=" O HIS S 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR S 244 " --> pdb=" O PHE S 281 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA S 318 " --> pdb=" O ILE S 282 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR S 319 " --> pdb=" O PRO S 208 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU S 210 " --> pdb=" O THR S 319 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 368 through 370 removed outlier: 6.840A pdb=" N SER S 369 " --> pdb=" O VAL S 475 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'S' and resid 573 through 577 removed outlier: 6.349A pdb=" N ILE S 574 " --> pdb=" O LEU S 619 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP S 621 " --> pdb=" O ILE S 574 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU S 576 " --> pdb=" O ASP S 621 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 642 through 644 Processing sheet with id=AH5, first strand: chain 'S' and resid 744 through 748 2458 hydrogen bonds defined for protein. 7131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.31 Time building geometry restraints manager: 10.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16103 1.34 - 1.46: 9216 1.46 - 1.58: 22234 1.58 - 1.70: 44 1.70 - 1.81: 308 Bond restraints: 47905 Sorted by residual: bond pdb=" C LYS T 305 " pdb=" N PRO T 306 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.30e-02 5.92e+03 3.85e+00 bond pdb=" C ILE O 490 " pdb=" N PRO O 491 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.85e+00 bond pdb=" C LYS P 305 " pdb=" N PRO P 306 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.30e-02 5.92e+03 1.82e+00 bond pdb=" CA GLU P 236 " pdb=" CB GLU P 236 " ideal model delta sigma weight residual 1.513 1.545 -0.031 2.59e-02 1.49e+03 1.48e+00 bond pdb=" CG GLU L 185 " pdb=" CD GLU L 185 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.47e+00 ... (remaining 47900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 64007 2.23 - 4.46: 616 4.46 - 6.69: 95 6.69 - 8.92: 6 8.92 - 11.15: 5 Bond angle restraints: 64729 Sorted by residual: angle pdb=" C ILE R 298 " pdb=" N ASP R 299 " pdb=" CA ASP R 299 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" C ALA L 131 " pdb=" CA ALA L 131 " pdb=" CB ALA L 131 " ideal model delta sigma weight residual 117.23 110.23 7.00 1.36e+00 5.41e-01 2.65e+01 angle pdb=" C ALA H 131 " pdb=" CA ALA H 131 " pdb=" CB ALA H 131 " ideal model delta sigma weight residual 117.23 110.33 6.90 1.36e+00 5.41e-01 2.57e+01 angle pdb=" C GLU Q 295 " pdb=" CA GLU Q 295 " pdb=" CB GLU Q 295 " ideal model delta sigma weight residual 116.63 110.86 5.77 1.16e+00 7.43e-01 2.47e+01 angle pdb=" C VAL S 196 " pdb=" N MET S 197 " pdb=" CA MET S 197 " ideal model delta sigma weight residual 121.58 113.70 7.88 1.95e+00 2.63e-01 1.63e+01 ... (remaining 64724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 29033 35.01 - 70.02: 515 70.02 - 105.02: 64 105.02 - 140.03: 6 140.03 - 175.04: 9 Dihedral angle restraints: 29627 sinusoidal: 12265 harmonic: 17362 Sorted by residual: dihedral pdb=" C5' ADP Q 901 " pdb=" O5' ADP Q 901 " pdb=" PA ADP Q 901 " pdb=" O2A ADP Q 901 " ideal model delta sinusoidal sigma weight residual -60.00 115.04 -175.04 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP P 901 " pdb=" O5' ADP P 901 " pdb=" PA ADP P 901 " pdb=" O2A ADP P 901 " ideal model delta sinusoidal sigma weight residual -60.00 114.93 -174.93 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP O 901 " pdb=" O5' ADP O 901 " pdb=" PA ADP O 901 " pdb=" O2A ADP O 901 " ideal model delta sinusoidal sigma weight residual -60.00 109.75 -169.74 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 29624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 5995 0.049 - 0.098: 1101 0.098 - 0.147: 356 0.147 - 0.196: 7 0.196 - 0.245: 1 Chirality restraints: 7460 Sorted by residual: chirality pdb=" CB ILE S 490 " pdb=" CA ILE S 490 " pdb=" CG1 ILE S 490 " pdb=" CG2 ILE S 490 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA GLU K 59 " pdb=" N GLU K 59 " pdb=" C GLU K 59 " pdb=" CB GLU K 59 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB ILE R 279 " pdb=" CA ILE R 279 " pdb=" CG1 ILE R 279 " pdb=" CG2 ILE R 279 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 7457 not shown) Planarity restraints: 8401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU S 262 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C GLU S 262 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU S 262 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU S 263 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS T 627 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO T 628 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO T 628 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO T 628 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN S 775 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C GLN S 775 " -0.034 2.00e-02 2.50e+03 pdb=" O GLN S 775 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG S 776 " 0.011 2.00e-02 2.50e+03 ... (remaining 8398 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 529 2.63 - 3.20: 42956 3.20 - 3.77: 73173 3.77 - 4.33: 98969 4.33 - 4.90: 166388 Nonbonded interactions: 382015 Sorted by model distance: nonbonded pdb=" O3B ATP T 902 " pdb="MG MG T 903 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR R 320 " pdb=" OE1 GLU R 323 " model vdw 2.069 3.040 nonbonded pdb=" O2G ATP S 902 " pdb="MG MG S 903 " model vdw 2.099 2.170 nonbonded pdb=" O2B ATP O 902 " pdb="MG MG O 903 " model vdw 2.114 2.170 nonbonded pdb=" O2G ATP R 902 " pdb="MG MG R 903 " model vdw 2.118 2.170 ... (remaining 382010 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 52 through 227) selection = (chain 'I' and resid 52 through 227) selection = (chain 'J' and resid 52 through 227) selection = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 52 through 227) selection = (chain 'N' and resid 52 through 227) } ncs_group { reference = (chain 'O' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 291 or resid 297 through 816 o \ r resid 902 through 903)) selection = (chain 'P' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 291 or resid 297 through 667 o \ r resid 688 through 816 or resid 902 through 903)) selection = (chain 'Q' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 291 or resid 297 through 667 o \ r resid 688 through 816 or resid 902 through 903)) selection = (chain 'R' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 291 or resid 297 through 667 o \ r resid 688 through 816 or resid 902 through 903)) selection = (chain 'S' and (resid 164 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 667 or resid 688 through 816 o \ r resid 902 through 903)) selection = (chain 'T' and (resid 164 through 291 or resid 297 through 667 or resid 688 thro \ ugh 816 or resid 902 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.060 Extract box with map and model: 1.440 Check model and map are aligned: 0.270 Set scattering table: 0.340 Process input model: 81.520 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 0.038 47905 Z= 0.145 Angle : 0.546 11.150 64729 Z= 0.282 Chirality : 0.041 0.245 7460 Planarity : 0.003 0.050 8401 Dihedral : 14.649 175.040 18417 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 0.02 % Allowed : 0.24 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.11), residues: 5962 helix: 1.59 (0.10), residues: 3111 sheet: 0.33 (0.17), residues: 847 loop : -0.42 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 189 HIS 0.004 0.001 HIS T 327 PHE 0.018 0.001 PHE R 810 TYR 0.017 0.001 TYR A 98 ARG 0.008 0.000 ARG J 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1353 time to evaluate : 4.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.7758 (t0) cc_final: 0.7495 (t0) REVERT: A 58 ASN cc_start: 0.7674 (m110) cc_final: 0.7343 (m110) REVERT: B 42 ASN cc_start: 0.8004 (m-40) cc_final: 0.7530 (m-40) REVERT: B 177 ILE cc_start: 0.7117 (mt) cc_final: 0.6913 (mp) REVERT: C 48 LEU cc_start: 0.8108 (tp) cc_final: 0.7705 (tt) REVERT: C 90 MET cc_start: 0.8004 (mmp) cc_final: 0.7714 (mmm) REVERT: C 141 SER cc_start: 0.8978 (p) cc_final: 0.8639 (t) REVERT: C 191 ASP cc_start: 0.7225 (p0) cc_final: 0.6914 (p0) REVERT: D 54 ASP cc_start: 0.7497 (m-30) cc_final: 0.7187 (m-30) REVERT: D 58 ASN cc_start: 0.7858 (m110) cc_final: 0.7534 (m-40) REVERT: D 73 LYS cc_start: 0.8228 (mppt) cc_final: 0.7925 (mppt) REVERT: D 134 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7069 (mt-10) REVERT: D 191 ASP cc_start: 0.7887 (p0) cc_final: 0.7665 (p0) REVERT: E 182 ARG cc_start: 0.7610 (ttm110) cc_final: 0.7178 (mtm-85) REVERT: E 185 ASP cc_start: 0.7796 (t70) cc_final: 0.7547 (t0) REVERT: E 191 ASP cc_start: 0.6675 (p0) cc_final: 0.6360 (p0) REVERT: F 37 TYR cc_start: 0.7577 (m-10) cc_final: 0.7348 (m-10) REVERT: F 38 ASN cc_start: 0.7356 (t0) cc_final: 0.7059 (m110) REVERT: F 53 ASP cc_start: 0.5972 (p0) cc_final: 0.5249 (p0) REVERT: F 58 ASN cc_start: 0.7697 (m110) cc_final: 0.7412 (m-40) REVERT: F 94 ASP cc_start: 0.7871 (t70) cc_final: 0.7582 (t0) REVERT: F 120 SER cc_start: 0.8049 (p) cc_final: 0.7813 (m) REVERT: G 70 ASP cc_start: 0.8263 (t0) cc_final: 0.7941 (t0) REVERT: G 202 ASP cc_start: 0.7592 (m-30) cc_final: 0.7272 (m-30) REVERT: H 76 ASP cc_start: 0.7547 (m-30) cc_final: 0.7301 (m-30) REVERT: H 226 THR cc_start: 0.8563 (p) cc_final: 0.8177 (p) REVERT: H 229 MET cc_start: 0.6988 (mpp) cc_final: 0.6647 (mpp) REVERT: I 56 LYS cc_start: 0.6988 (mttt) cc_final: 0.6681 (tptp) REVERT: I 161 GLU cc_start: 0.8301 (pp20) cc_final: 0.7606 (pp20) REVERT: I 229 MET cc_start: 0.8616 (mmm) cc_final: 0.8378 (mpp) REVERT: K 108 THR cc_start: 0.7904 (m) cc_final: 0.7251 (p) REVERT: K 112 ASP cc_start: 0.7679 (m-30) cc_final: 0.7322 (m-30) REVERT: K 204 GLU cc_start: 0.7846 (tp30) cc_final: 0.7627 (tp30) REVERT: L 71 ASP cc_start: 0.8115 (m-30) cc_final: 0.7856 (m-30) REVERT: L 75 ASN cc_start: 0.7834 (m-40) cc_final: 0.7535 (m-40) REVERT: L 112 ASP cc_start: 0.7224 (m-30) cc_final: 0.6913 (m-30) REVERT: L 118 LYS cc_start: 0.8483 (ptpt) cc_final: 0.8049 (ptmt) REVERT: L 213 ASP cc_start: 0.7245 (m-30) cc_final: 0.7001 (m-30) REVERT: L 225 SER cc_start: 0.8022 (t) cc_final: 0.7730 (p) REVERT: M 164 ARG cc_start: 0.7624 (tpp-160) cc_final: 0.7092 (mmm160) REVERT: N 198 LYS cc_start: 0.7278 (tppp) cc_final: 0.7035 (tptp) REVERT: R 239 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7793 (mmpt) REVERT: R 247 ASP cc_start: 0.8320 (t0) cc_final: 0.7964 (t0) REVERT: R 262 GLU cc_start: 0.7790 (mp0) cc_final: 0.7406 (mp0) REVERT: R 270 LYS cc_start: 0.8168 (tppt) cc_final: 0.7961 (ttmm) REVERT: R 275 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7726 (mmm-85) REVERT: R 723 ASP cc_start: 0.7831 (m-30) cc_final: 0.7618 (m-30) REVERT: R 743 ASP cc_start: 0.7994 (t0) cc_final: 0.7650 (t0) REVERT: Q 499 GLU cc_start: 0.7607 (tt0) cc_final: 0.7350 (tt0) REVERT: Q 505 ARG cc_start: 0.7542 (mtm110) cc_final: 0.7196 (ptp90) REVERT: Q 697 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7600 (mm-30) REVERT: P 166 VAL cc_start: 0.7968 (t) cc_final: 0.7712 (t) REVERT: P 256 ARG cc_start: 0.8220 (ptm160) cc_final: 0.7910 (ttp-110) REVERT: P 747 GLU cc_start: 0.7662 (tp30) cc_final: 0.7401 (tp30) REVERT: P 748 LEU cc_start: 0.8640 (mt) cc_final: 0.8151 (mt) REVERT: P 758 LYS cc_start: 0.8520 (tmmt) cc_final: 0.8297 (ptpt) REVERT: P 776 ARG cc_start: 0.7928 (ptp-110) cc_final: 0.7466 (ptm160) REVERT: P 784 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7902 (mt-10) REVERT: P 798 VAL cc_start: 0.8360 (t) cc_final: 0.8140 (m) REVERT: O 263 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7277 (tm-30) REVERT: O 267 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8318 (ttmm) REVERT: O 270 LYS cc_start: 0.8516 (tptm) cc_final: 0.8209 (tptm) REVERT: O 321 LEU cc_start: 0.8551 (tp) cc_final: 0.8335 (tm) REVERT: O 325 ARG cc_start: 0.7615 (ptm-80) cc_final: 0.7326 (ptm160) REVERT: O 329 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7380 (mt-10) REVERT: O 385 TYR cc_start: 0.8058 (m-80) cc_final: 0.7808 (m-80) REVERT: O 406 MET cc_start: 0.8151 (tpp) cc_final: 0.7901 (tpp) REVERT: O 506 MET cc_start: 0.6908 (ttt) cc_final: 0.5862 (ptm) REVERT: O 608 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7716 (mm-30) REVERT: O 621 ASP cc_start: 0.8168 (t70) cc_final: 0.7858 (t0) REVERT: O 635 LEU cc_start: 0.8862 (mt) cc_final: 0.8600 (mm) REVERT: O 693 LYS cc_start: 0.8339 (ptmt) cc_final: 0.7937 (pttp) REVERT: O 758 LYS cc_start: 0.8693 (mptt) cc_final: 0.8486 (mttt) REVERT: O 759 LYS cc_start: 0.8589 (tppp) cc_final: 0.8180 (tptt) REVERT: O 772 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7607 (tpp-160) REVERT: O 776 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7588 (ttp80) REVERT: O 784 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7106 (mm-30) REVERT: O 787 LEU cc_start: 0.8074 (mm) cc_final: 0.7604 (mt) REVERT: O 800 ASP cc_start: 0.7734 (m-30) cc_final: 0.7523 (t70) REVERT: O 810 PHE cc_start: 0.8200 (m-80) cc_final: 0.7923 (m-10) REVERT: T 207 ASN cc_start: 0.8201 (m110) cc_final: 0.7734 (m110) REVERT: T 223 GLU cc_start: 0.8610 (mp0) cc_final: 0.8255 (mp0) REVERT: T 242 HIS cc_start: 0.8022 (m-70) cc_final: 0.7372 (m170) REVERT: T 271 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8458 (tm-30) REVERT: T 272 ILE cc_start: 0.9172 (pt) cc_final: 0.8773 (pp) REVERT: T 304 LEU cc_start: 0.8473 (mm) cc_final: 0.7980 (pp) REVERT: T 322 ASP cc_start: 0.8630 (p0) cc_final: 0.8334 (p0) REVERT: T 408 ILE cc_start: 0.7345 (pt) cc_final: 0.7030 (pt) REVERT: T 576 LEU cc_start: 0.8404 (mt) cc_final: 0.8156 (mp) REVERT: T 619 LEU cc_start: 0.8343 (tp) cc_final: 0.7930 (tm) REVERT: T 642 ARG cc_start: 0.8081 (mtm110) cc_final: 0.7880 (mtm110) REVERT: T 660 MET cc_start: 0.8286 (mtm) cc_final: 0.8052 (mpp) REVERT: T 687 TYR cc_start: 0.7540 (t80) cc_final: 0.6822 (t80) REVERT: T 761 TYR cc_start: 0.8123 (t80) cc_final: 0.7129 (t80) REVERT: T 772 ARG cc_start: 0.8220 (mmt180) cc_final: 0.7873 (mmm160) REVERT: S 184 ASP cc_start: 0.7372 (p0) cc_final: 0.6941 (p0) REVERT: S 191 LYS cc_start: 0.7613 (mppt) cc_final: 0.7392 (mppt) REVERT: S 205 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7383 (mtpm) REVERT: S 241 LYS cc_start: 0.7187 (mmmt) cc_final: 0.6970 (mmmt) REVERT: S 282 ILE cc_start: 0.8423 (mm) cc_final: 0.8216 (mm) REVERT: S 307 MET cc_start: 0.8691 (mmp) cc_final: 0.8479 (mmm) REVERT: S 310 ARG cc_start: 0.8508 (mmt180) cc_final: 0.7925 (ttp-110) REVERT: S 401 GLU cc_start: 0.8299 (tp30) cc_final: 0.7980 (tp30) REVERT: S 404 SER cc_start: 0.8318 (t) cc_final: 0.8040 (p) REVERT: S 532 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.7307 (tmm160) REVERT: S 539 LYS cc_start: 0.7995 (tmmt) cc_final: 0.7496 (ttpp) REVERT: S 540 ARG cc_start: 0.7860 (mtp180) cc_final: 0.6794 (mtp-110) REVERT: S 600 TYR cc_start: 0.8302 (t80) cc_final: 0.8100 (t80) REVERT: S 615 PHE cc_start: 0.8523 (m-80) cc_final: 0.8250 (m-80) REVERT: S 636 GLN cc_start: 0.7933 (mt0) cc_final: 0.7621 (mt0) REVERT: S 642 ARG cc_start: 0.7615 (ptp-110) cc_final: 0.7136 (ptp-110) REVERT: S 692 ASN cc_start: 0.7841 (m110) cc_final: 0.7520 (m110) outliers start: 1 outliers final: 4 residues processed: 1354 average time/residue: 1.4989 time to fit residues: 2436.2475 Evaluate side-chains 1014 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1010 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain T residue 383 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 499 optimal weight: 5.9990 chunk 448 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 464 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 chunk 345 optimal weight: 3.9990 chunk 537 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 171 GLN B 63 GLN B 101 ASN C 97 GLN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN D 116 GLN D 139 GLN F 97 GLN G 97 GLN G 101 ASN G 175 GLN G 179 GLN H 166 GLN H 183 GLN K 166 GLN M 222 GLN N 156 HIS R 173 ASN R 286 HIS P 169 GLN O 242 HIS O 701 HIS O 708 ASN ** T 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 ASN S 700 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.113095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.088152 restraints weight = 78611.438| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.74 r_work: 0.3477 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 47905 Z= 0.296 Angle : 0.625 10.659 64729 Z= 0.320 Chirality : 0.044 0.229 7460 Planarity : 0.005 0.051 8401 Dihedral : 10.318 179.723 6867 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.14 % Favored : 95.69 % Rotamer: Outliers : 3.16 % Allowed : 12.79 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.11), residues: 5962 helix: 1.57 (0.09), residues: 3185 sheet: 0.53 (0.17), residues: 769 loop : -0.49 (0.15), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 189 HIS 0.014 0.001 HIS O 286 PHE 0.021 0.002 PHE Q 631 TYR 0.017 0.002 TYR Q 362 ARG 0.015 0.001 ARG S 540 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1024 time to evaluate : 4.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.8500 (m-40) cc_final: 0.8258 (m110) REVERT: B 194 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8064 (mt-10) REVERT: E 139 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8000 (pp30) REVERT: G 205 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7871 (ptm) REVERT: H 60 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: H 115 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: H 229 MET cc_start: 0.8021 (mpp) cc_final: 0.7644 (mpp) REVERT: I 56 LYS cc_start: 0.7756 (mttt) cc_final: 0.7379 (ttmt) REVERT: I 161 GLU cc_start: 0.8429 (pp20) cc_final: 0.8116 (pp20) REVERT: I 229 MET cc_start: 0.8858 (mmm) cc_final: 0.8589 (mpp) REVERT: J 146 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8829 (ptp) REVERT: J 222 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: K 222 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8400 (pt0) REVERT: L 112 ASP cc_start: 0.8063 (m-30) cc_final: 0.7831 (m-30) REVERT: M 204 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7683 (mm-30) REVERT: R 182 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8781 (mtmp) REVERT: R 262 GLU cc_start: 0.8292 (mp0) cc_final: 0.7990 (mp0) REVERT: R 305 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8380 (ttmm) REVERT: R 743 ASP cc_start: 0.8347 (t0) cc_final: 0.8097 (t0) REVERT: Q 743 ASP cc_start: 0.8419 (t0) cc_final: 0.8182 (t0) REVERT: P 240 ASP cc_start: 0.8247 (m-30) cc_final: 0.8000 (m-30) REVERT: P 494 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8718 (tmmt) REVERT: P 787 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8659 (mm) REVERT: O 263 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8050 (tm-30) REVERT: O 267 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8806 (ttmt) REVERT: O 310 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7440 (ttm110) REVERT: O 321 LEU cc_start: 0.8828 (tp) cc_final: 0.8610 (tm) REVERT: O 325 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.7659 (ptm160) REVERT: O 367 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7450 (mmm160) REVERT: O 405 ARG cc_start: 0.8455 (tpt170) cc_final: 0.8001 (tpm170) REVERT: O 602 GLU cc_start: 0.8288 (pm20) cc_final: 0.7993 (pm20) REVERT: O 690 MET cc_start: 0.7230 (pmm) cc_final: 0.6479 (pmm) REVERT: O 755 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8292 (pp) REVERT: O 759 LYS cc_start: 0.8258 (tppp) cc_final: 0.7992 (tptp) REVERT: O 772 ARG cc_start: 0.8389 (tpp80) cc_final: 0.8007 (tpp-160) REVERT: O 775 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7408 (tm130) REVERT: O 776 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7565 (ttp80) REVERT: O 787 LEU cc_start: 0.8102 (mm) cc_final: 0.7869 (mt) REVERT: T 170 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7273 (t80) REVERT: T 207 ASN cc_start: 0.8499 (m110) cc_final: 0.8130 (m110) REVERT: T 223 GLU cc_start: 0.8461 (mp0) cc_final: 0.8182 (mp0) REVERT: T 244 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6688 (t80) REVERT: T 271 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8461 (tm-30) REVERT: T 272 ILE cc_start: 0.9072 (pt) cc_final: 0.8626 (pp) REVERT: T 304 LEU cc_start: 0.8506 (mm) cc_final: 0.7914 (pp) REVERT: T 305 LYS cc_start: 0.8050 (tppt) cc_final: 0.7804 (tptp) REVERT: T 401 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7778 (tt0) REVERT: T 502 ARG cc_start: 0.7452 (mmm160) cc_final: 0.7167 (mmm160) REVERT: T 619 LEU cc_start: 0.8717 (tp) cc_final: 0.8368 (tm) REVERT: T 634 LEU cc_start: 0.7920 (mt) cc_final: 0.7649 (mp) REVERT: T 643 LEU cc_start: 0.7212 (mt) cc_final: 0.6467 (pp) REVERT: T 687 TYR cc_start: 0.7600 (t80) cc_final: 0.7364 (t80) REVERT: T 690 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8296 (ptt) REVERT: T 734 LYS cc_start: 0.8974 (mttt) cc_final: 0.8708 (mppt) REVERT: T 742 ARG cc_start: 0.8413 (tpt90) cc_final: 0.7825 (tpm170) REVERT: T 744 MET cc_start: 0.7324 (mmt) cc_final: 0.6925 (mmt) REVERT: T 761 TYR cc_start: 0.8030 (t80) cc_final: 0.7244 (t80) REVERT: S 184 ASP cc_start: 0.7342 (p0) cc_final: 0.7067 (p0) REVERT: S 191 LYS cc_start: 0.7793 (mppt) cc_final: 0.7592 (mppt) REVERT: S 205 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7797 (mtpp) REVERT: S 310 ARG cc_start: 0.8329 (mmt180) cc_final: 0.8017 (ttp-110) REVERT: S 316 ILE cc_start: 0.8785 (mp) cc_final: 0.8533 (mp) REVERT: S 354 ILE cc_start: 0.8726 (mt) cc_final: 0.8502 (tt) REVERT: S 605 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: S 635 LEU cc_start: 0.8652 (tp) cc_final: 0.8370 (tm) REVERT: S 642 ARG cc_start: 0.7932 (ptp-110) cc_final: 0.7591 (ptp-110) outliers start: 159 outliers final: 56 residues processed: 1095 average time/residue: 1.5645 time to fit residues: 2045.6658 Evaluate side-chains 1013 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 943 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 207 LYS Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain K residue 181 ARG Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 323 GLU Chi-restraints excluded: chain Q residue 373 GLU Chi-restraints excluded: chain Q residue 601 GLU Chi-restraints excluded: chain P residue 494 LYS Chi-restraints excluded: chain P residue 787 LEU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 591 PHE Chi-restraints excluded: chain O residue 707 LEU Chi-restraints excluded: chain O residue 719 LEU Chi-restraints excluded: chain O residue 726 LYS Chi-restraints excluded: chain O residue 732 ILE Chi-restraints excluded: chain O residue 755 LEU Chi-restraints excluded: chain O residue 797 VAL Chi-restraints excluded: chain T residue 170 PHE Chi-restraints excluded: chain T residue 244 TYR Chi-restraints excluded: chain T residue 383 ASP Chi-restraints excluded: chain T residue 486 THR Chi-restraints excluded: chain T residue 690 MET Chi-restraints excluded: chain T residue 798 VAL Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain S residue 280 LEU Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 409 ARG Chi-restraints excluded: chain S residue 605 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 568 optimal weight: 0.0040 chunk 276 optimal weight: 0.8980 chunk 322 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 583 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 550 optimal weight: 7.9990 chunk 414 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN G 101 ASN H 128 GLN H 183 GLN J 183 GLN M 183 GLN N 156 HIS R 173 ASN P 169 GLN P 700 GLN O 366 HIS O 701 HIS ** T 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 ASN S 674 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.113581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.088563 restraints weight = 78956.208| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.75 r_work: 0.3483 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 47905 Z= 0.199 Angle : 0.573 11.112 64729 Z= 0.290 Chirality : 0.042 0.225 7460 Planarity : 0.004 0.050 8401 Dihedral : 9.913 178.115 6861 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.62 % Favored : 96.26 % Rotamer: Outliers : 2.96 % Allowed : 15.22 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.11), residues: 5962 helix: 1.74 (0.09), residues: 3194 sheet: 0.38 (0.17), residues: 818 loop : -0.45 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 189 HIS 0.005 0.001 HIS O 286 PHE 0.033 0.001 PHE O 565 TYR 0.015 0.001 TYR O 324 ARG 0.014 0.000 ARG R 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 973 time to evaluate : 4.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.8500 (m-40) cc_final: 0.8238 (m110) REVERT: E 66 LEU cc_start: 0.8772 (tt) cc_final: 0.8557 (tt) REVERT: E 203 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: F 39 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8154 (ttp80) REVERT: H 60 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: H 115 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: H 229 MET cc_start: 0.8003 (mpp) cc_final: 0.7616 (mpp) REVERT: I 56 LYS cc_start: 0.7747 (mttt) cc_final: 0.7537 (mtmt) REVERT: J 222 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8142 (pt0) REVERT: K 222 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: L 112 ASP cc_start: 0.8047 (m-30) cc_final: 0.7843 (m-30) REVERT: M 190 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8518 (tptm) REVERT: M 207 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8598 (tttp) REVERT: N 181 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7690 (ttm-80) REVERT: R 262 GLU cc_start: 0.8292 (mp0) cc_final: 0.7993 (mp0) REVERT: R 305 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8489 (ttmm) REVERT: R 743 ASP cc_start: 0.8308 (t0) cc_final: 0.7991 (t0) REVERT: Q 733 ASP cc_start: 0.8568 (t0) cc_final: 0.8264 (t0) REVERT: Q 743 ASP cc_start: 0.8428 (t0) cc_final: 0.8167 (t0) REVERT: P 240 ASP cc_start: 0.8177 (m-30) cc_final: 0.7952 (m-30) REVERT: P 494 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8713 (tmmt) REVERT: P 570 GLU cc_start: 0.8045 (tt0) cc_final: 0.7735 (tt0) REVERT: P 776 ARG cc_start: 0.8103 (ptp-110) cc_final: 0.7864 (ptm160) REVERT: P 787 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8672 (mm) REVERT: P 791 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7297 (mt) REVERT: O 234 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8352 (t) REVERT: O 263 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7985 (tm-30) REVERT: O 267 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8809 (ttmt) REVERT: O 321 LEU cc_start: 0.8894 (tp) cc_final: 0.8674 (tm) REVERT: O 325 ARG cc_start: 0.8003 (ptm-80) cc_final: 0.7757 (ptm-80) REVERT: O 405 ARG cc_start: 0.8364 (tpt170) cc_final: 0.7967 (tpm170) REVERT: O 602 GLU cc_start: 0.8275 (pm20) cc_final: 0.8052 (pm20) REVERT: O 755 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8146 (pp) REVERT: O 759 LYS cc_start: 0.8229 (tppp) cc_final: 0.7908 (tptp) REVERT: O 772 ARG cc_start: 0.8336 (tpp80) cc_final: 0.8090 (tpp-160) REVERT: O 775 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7091 (tm130) REVERT: O 787 LEU cc_start: 0.8106 (mm) cc_final: 0.7845 (mt) REVERT: T 170 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7186 (t80) REVERT: T 207 ASN cc_start: 0.8510 (m110) cc_final: 0.8097 (m110) REVERT: T 223 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: T 244 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6218 (t80) REVERT: T 271 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8371 (tm-30) REVERT: T 272 ILE cc_start: 0.9020 (pt) cc_final: 0.8635 (pp) REVERT: T 304 LEU cc_start: 0.8504 (mm) cc_final: 0.7958 (pp) REVERT: T 305 LYS cc_start: 0.8053 (tppt) cc_final: 0.7700 (tptp) REVERT: T 401 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: T 502 ARG cc_start: 0.7391 (mmm160) cc_final: 0.6955 (mmm160) REVERT: T 613 LYS cc_start: 0.8035 (pttm) cc_final: 0.7652 (tptt) REVERT: T 619 LEU cc_start: 0.8721 (tp) cc_final: 0.8464 (tm) REVERT: T 631 PHE cc_start: 0.7435 (m-10) cc_final: 0.7196 (m-10) REVERT: T 642 ARG cc_start: 0.7961 (mtm110) cc_final: 0.7548 (ptt90) REVERT: T 643 LEU cc_start: 0.7277 (mt) cc_final: 0.6550 (pp) REVERT: T 734 LYS cc_start: 0.8981 (mttt) cc_final: 0.8727 (mppt) REVERT: T 742 ARG cc_start: 0.8395 (tpt90) cc_final: 0.7851 (tpm170) REVERT: T 744 MET cc_start: 0.7158 (mmt) cc_final: 0.6922 (mmm) REVERT: T 761 TYR cc_start: 0.7993 (t80) cc_final: 0.7208 (t80) REVERT: S 184 ASP cc_start: 0.7326 (p0) cc_final: 0.7055 (p0) REVERT: S 205 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7850 (mtpm) REVERT: S 279 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7724 (tp) REVERT: S 307 MET cc_start: 0.8406 (mmm) cc_final: 0.8047 (mmm) REVERT: S 310 ARG cc_start: 0.8275 (mmt180) cc_final: 0.8038 (ttp-110) REVERT: S 609 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8667 (mtmt) REVERT: S 635 LEU cc_start: 0.8724 (tp) cc_final: 0.8447 (tm) REVERT: S 642 ARG cc_start: 0.7906 (ptp-110) cc_final: 0.7581 (ptp-110) REVERT: S 702 PHE cc_start: 0.7403 (m-10) cc_final: 0.7162 (m-10) REVERT: S 709 ARG cc_start: 0.7316 (tpt-90) cc_final: 0.7046 (tpt-90) outliers start: 149 outliers final: 54 residues processed: 1044 average time/residue: 1.6235 time to fit residues: 2014.9837 Evaluate side-chains 1012 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 939 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 190 LYS Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain R residue 590 LEU Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 323 GLU Chi-restraints excluded: chain Q residue 601 GLU Chi-restraints excluded: chain P residue 373 GLU Chi-restraints excluded: chain P residue 494 LYS Chi-restraints excluded: chain P residue 787 LEU Chi-restraints excluded: chain P residue 791 LEU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 591 PHE Chi-restraints excluded: chain O residue 719 LEU Chi-restraints excluded: chain O residue 726 LYS Chi-restraints excluded: chain O residue 755 LEU Chi-restraints excluded: chain O residue 797 VAL Chi-restraints excluded: chain T residue 170 PHE Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 244 TYR Chi-restraints excluded: chain T residue 362 TYR Chi-restraints excluded: chain T residue 401 GLU Chi-restraints excluded: chain T residue 486 THR Chi-restraints excluded: chain T residue 546 ILE Chi-restraints excluded: chain T residue 707 LEU Chi-restraints excluded: chain T residue 733 ASP Chi-restraints excluded: chain S residue 279 ILE Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 609 LYS Chi-restraints excluded: chain S residue 621 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 513 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 372 optimal weight: 7.9990 chunk 429 optimal weight: 20.0000 chunk 231 optimal weight: 4.9990 chunk 490 optimal weight: 9.9990 chunk 564 optimal weight: 0.9980 chunk 374 optimal weight: 0.8980 chunk 383 optimal weight: 0.0010 chunk 283 optimal weight: 3.9990 chunk 485 optimal weight: 0.8980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN B 101 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN D 42 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 128 GLN H 183 GLN M 122 GLN M 222 GLN N 156 HIS R 169 GLN R 173 ASN R 198 GLN P 700 GLN O 701 HIS ** T 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 ASN S 674 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.114032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.089141 restraints weight = 78504.748| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.74 r_work: 0.3493 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 47905 Z= 0.172 Angle : 0.560 10.725 64729 Z= 0.282 Chirality : 0.041 0.220 7460 Planarity : 0.004 0.050 8401 Dihedral : 9.506 177.133 6859 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 2.98 % Allowed : 16.85 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.11), residues: 5962 helix: 1.86 (0.09), residues: 3202 sheet: 0.49 (0.17), residues: 811 loop : -0.43 (0.15), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 189 HIS 0.007 0.001 HIS O 286 PHE 0.017 0.001 PHE O 565 TYR 0.019 0.001 TYR H 159 ARG 0.012 0.000 ARG R 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 951 time to evaluate : 4.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.8500 (m-40) cc_final: 0.8248 (m110) REVERT: D 164 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7750 (mmp-170) REVERT: E 66 LEU cc_start: 0.8765 (tt) cc_final: 0.8563 (tp) REVERT: E 203 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: F 39 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8148 (ttp80) REVERT: F 197 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: H 115 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: H 229 MET cc_start: 0.8000 (mpp) cc_final: 0.7607 (mpp) REVERT: I 56 LYS cc_start: 0.7701 (mttt) cc_final: 0.7486 (mtmt) REVERT: I 228 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8407 (mttm) REVERT: J 222 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: K 222 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8454 (pt0) REVERT: L 112 ASP cc_start: 0.7971 (m-30) cc_final: 0.7767 (m-30) REVERT: N 181 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7634 (ttm-80) REVERT: R 182 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8477 (mtmm) REVERT: R 262 GLU cc_start: 0.8283 (mp0) cc_final: 0.8013 (mp0) REVERT: R 305 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8510 (ttmm) REVERT: R 335 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7452 (mp0) REVERT: R 522 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8321 (mtmm) REVERT: R 743 ASP cc_start: 0.8257 (t0) cc_final: 0.7948 (t0) REVERT: Q 697 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8166 (mm-30) REVERT: Q 733 ASP cc_start: 0.8530 (t0) cc_final: 0.8247 (t0) REVERT: Q 743 ASP cc_start: 0.8410 (t0) cc_final: 0.8196 (t0) REVERT: P 240 ASP cc_start: 0.8139 (m-30) cc_final: 0.7924 (m-30) REVERT: P 570 GLU cc_start: 0.8009 (tt0) cc_final: 0.7716 (tt0) REVERT: P 791 LEU cc_start: 0.7512 (mp) cc_final: 0.7235 (mt) REVERT: O 234 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8278 (t) REVERT: O 263 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8005 (tm-30) REVERT: O 267 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8804 (ttmt) REVERT: O 307 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7600 (mtm) REVERT: O 325 ARG cc_start: 0.7994 (ptm-80) cc_final: 0.7663 (ptm-80) REVERT: O 329 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7663 (mt-10) REVERT: O 405 ARG cc_start: 0.8332 (tpt170) cc_final: 0.7964 (tpm170) REVERT: O 506 MET cc_start: 0.6188 (ttp) cc_final: 0.5232 (ptm) REVERT: O 532 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7872 (tmt170) REVERT: O 602 GLU cc_start: 0.8254 (pm20) cc_final: 0.7970 (pm20) REVERT: O 639 GLU cc_start: 0.8412 (tt0) cc_final: 0.8190 (tt0) REVERT: O 755 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8113 (pp) REVERT: O 759 LYS cc_start: 0.8254 (tppp) cc_final: 0.7952 (tptp) REVERT: O 775 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7109 (tm130) REVERT: O 787 LEU cc_start: 0.8123 (mm) cc_final: 0.7871 (mt) REVERT: T 170 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7298 (t80) REVERT: T 207 ASN cc_start: 0.8500 (m110) cc_final: 0.8175 (m110) REVERT: T 223 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: T 244 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.6337 (t80) REVERT: T 271 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8346 (tm-30) REVERT: T 272 ILE cc_start: 0.9001 (pt) cc_final: 0.8606 (pp) REVERT: T 304 LEU cc_start: 0.8504 (mm) cc_final: 0.8002 (pp) REVERT: T 305 LYS cc_start: 0.8052 (tppt) cc_final: 0.7697 (tptp) REVERT: T 401 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: T 502 ARG cc_start: 0.7432 (mmm160) cc_final: 0.6994 (mmm160) REVERT: T 613 LYS cc_start: 0.7998 (pttm) cc_final: 0.7618 (tptt) REVERT: T 619 LEU cc_start: 0.8758 (tp) cc_final: 0.8457 (tm) REVERT: T 642 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7584 (ptt90) REVERT: T 643 LEU cc_start: 0.7248 (mt) cc_final: 0.6521 (pp) REVERT: T 687 TYR cc_start: 0.7889 (t80) cc_final: 0.7679 (t80) REVERT: T 733 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: T 742 ARG cc_start: 0.8342 (tpt90) cc_final: 0.7815 (tpm170) REVERT: T 744 MET cc_start: 0.7136 (mmt) cc_final: 0.6907 (mmm) REVERT: T 761 TYR cc_start: 0.8008 (t80) cc_final: 0.7232 (t80) REVERT: S 184 ASP cc_start: 0.7329 (p0) cc_final: 0.7069 (p0) REVERT: S 205 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7718 (mtpp) REVERT: S 279 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7651 (tp) REVERT: S 281 PHE cc_start: 0.8512 (t80) cc_final: 0.8204 (t80) REVERT: S 307 MET cc_start: 0.8398 (mmm) cc_final: 0.8005 (mmm) REVERT: S 310 ARG cc_start: 0.8262 (mmt180) cc_final: 0.8036 (ttp-110) REVERT: S 407 ARG cc_start: 0.7169 (ttm-80) cc_final: 0.6737 (ttm-80) REVERT: S 540 ARG cc_start: 0.8044 (mtp-110) cc_final: 0.7807 (mtp-110) REVERT: S 609 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8754 (mtmt) REVERT: S 635 LEU cc_start: 0.8702 (tp) cc_final: 0.8485 (tm) REVERT: S 639 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: S 642 ARG cc_start: 0.7946 (ptp-110) cc_final: 0.7619 (ptp-110) outliers start: 150 outliers final: 44 residues processed: 1033 average time/residue: 1.6011 time to fit residues: 1969.3277 Evaluate side-chains 986 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 921 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 522 LYS Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 323 GLU Chi-restraints excluded: chain Q residue 539 LYS Chi-restraints excluded: chain Q residue 601 GLU Chi-restraints excluded: chain P residue 795 HIS Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 591 PHE Chi-restraints excluded: chain O residue 719 LEU Chi-restraints excluded: chain O residue 755 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain O residue 797 VAL Chi-restraints excluded: chain T residue 170 PHE Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 244 TYR Chi-restraints excluded: chain T residue 401 GLU Chi-restraints excluded: chain T residue 733 ASP Chi-restraints excluded: chain S residue 279 ILE Chi-restraints excluded: chain S residue 280 LEU Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 381 LEU Chi-restraints excluded: chain S residue 601 GLU Chi-restraints excluded: chain S residue 609 LYS Chi-restraints excluded: chain S residue 639 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 451 optimal weight: 2.9990 chunk 391 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 270 optimal weight: 0.0000 chunk 181 optimal weight: 0.0270 chunk 298 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 570 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 494 optimal weight: 8.9990 overall best weight: 1.0246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 38 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN J 122 GLN J 183 GLN N 156 HIS R 173 ASN R 198 GLN R 686 ASN P 700 GLN O 701 HIS ** T 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 ASN S 674 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.113396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.088387 restraints weight = 78494.229| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.74 r_work: 0.3477 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 47905 Z= 0.195 Angle : 0.570 10.612 64729 Z= 0.286 Chirality : 0.042 0.217 7460 Planarity : 0.004 0.048 8401 Dihedral : 9.292 177.878 6859 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.06 % Rotamer: Outliers : 2.77 % Allowed : 17.67 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.11), residues: 5962 helix: 1.90 (0.09), residues: 3206 sheet: 0.53 (0.17), residues: 810 loop : -0.42 (0.15), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 189 HIS 0.008 0.001 HIS O 286 PHE 0.019 0.001 PHE O 261 TYR 0.017 0.001 TYR O 324 ARG 0.010 0.000 ARG P 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 944 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 164 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7791 (mmp-170) REVERT: E 203 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: F 197 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: H 115 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: H 229 MET cc_start: 0.8043 (mpp) cc_final: 0.7713 (mpp) REVERT: I 56 LYS cc_start: 0.7734 (mttt) cc_final: 0.7507 (mtmt) REVERT: I 228 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8502 (mttm) REVERT: J 222 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: K 222 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: L 112 ASP cc_start: 0.8014 (m-30) cc_final: 0.7807 (m-30) REVERT: M 190 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8522 (tptm) REVERT: N 181 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7608 (ttm-80) REVERT: R 182 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8577 (mtmm) REVERT: R 262 GLU cc_start: 0.8290 (mp0) cc_final: 0.8042 (mp0) REVERT: R 305 LYS cc_start: 0.8789 (mmmm) cc_final: 0.8520 (ttmm) REVERT: R 734 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8526 (mtpt) REVERT: R 743 ASP cc_start: 0.8257 (t0) cc_final: 0.7961 (t0) REVERT: Q 697 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8201 (mm-30) REVERT: Q 733 ASP cc_start: 0.8556 (t0) cc_final: 0.8283 (t0) REVERT: Q 743 ASP cc_start: 0.8427 (t0) cc_final: 0.8221 (t0) REVERT: P 240 ASP cc_start: 0.8172 (m-30) cc_final: 0.7951 (m-30) REVERT: P 570 GLU cc_start: 0.8004 (tt0) cc_final: 0.7722 (tt0) REVERT: P 791 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7411 (mt) REVERT: O 234 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8299 (t) REVERT: O 263 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7974 (tm-30) REVERT: O 267 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8787 (ttmt) REVERT: O 307 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7565 (mtm) REVERT: O 325 ARG cc_start: 0.7991 (ptm-80) cc_final: 0.7656 (ptm-80) REVERT: O 329 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7656 (mt-10) REVERT: O 405 ARG cc_start: 0.8378 (tpt170) cc_final: 0.8001 (tpm170) REVERT: O 506 MET cc_start: 0.6162 (ttp) cc_final: 0.5258 (ptm) REVERT: O 532 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7848 (tpt-90) REVERT: O 602 GLU cc_start: 0.8269 (pm20) cc_final: 0.8012 (pm20) REVERT: O 755 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8098 (pp) REVERT: O 759 LYS cc_start: 0.8266 (tppp) cc_final: 0.7951 (tptp) REVERT: O 775 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7193 (tm130) REVERT: O 787 LEU cc_start: 0.8175 (mm) cc_final: 0.7940 (mt) REVERT: T 170 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7300 (t80) REVERT: T 207 ASN cc_start: 0.8507 (m110) cc_final: 0.8159 (m110) REVERT: T 223 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: T 244 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6354 (t80) REVERT: T 271 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8321 (tm-30) REVERT: T 272 ILE cc_start: 0.8993 (pt) cc_final: 0.8590 (pp) REVERT: T 304 LEU cc_start: 0.8504 (mm) cc_final: 0.7987 (pp) REVERT: T 305 LYS cc_start: 0.8007 (tppt) cc_final: 0.7698 (tptp) REVERT: T 401 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: T 502 ARG cc_start: 0.7430 (mmm160) cc_final: 0.6988 (mmm160) REVERT: T 575 SER cc_start: 0.8714 (t) cc_final: 0.8369 (p) REVERT: T 613 LYS cc_start: 0.7983 (pttm) cc_final: 0.7601 (tptt) REVERT: T 619 LEU cc_start: 0.8737 (tp) cc_final: 0.8440 (tm) REVERT: T 642 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7617 (ptt90) REVERT: T 643 LEU cc_start: 0.7224 (mt) cc_final: 0.6459 (pp) REVERT: T 687 TYR cc_start: 0.7833 (t80) cc_final: 0.7584 (t80) REVERT: T 734 LYS cc_start: 0.8903 (mppt) cc_final: 0.8685 (mppt) REVERT: T 742 ARG cc_start: 0.8348 (tpt90) cc_final: 0.7817 (tpm170) REVERT: T 744 MET cc_start: 0.7243 (mmt) cc_final: 0.6969 (mmm) REVERT: T 761 TYR cc_start: 0.7997 (t80) cc_final: 0.7207 (t80) REVERT: S 184 ASP cc_start: 0.7339 (p0) cc_final: 0.7060 (p0) REVERT: S 205 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7757 (mtpp) REVERT: S 279 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7814 (tp) REVERT: S 281 PHE cc_start: 0.8684 (t80) cc_final: 0.8278 (t80) REVERT: S 286 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.6894 (p90) REVERT: S 307 MET cc_start: 0.8446 (mmm) cc_final: 0.7978 (mmm) REVERT: S 310 ARG cc_start: 0.8250 (mmt180) cc_final: 0.8031 (ttp-110) REVERT: S 319 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7660 (t) REVERT: S 354 ILE cc_start: 0.8748 (mt) cc_final: 0.8462 (tt) REVERT: S 609 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8752 (mtmt) REVERT: S 635 LEU cc_start: 0.8728 (tp) cc_final: 0.8468 (tm) REVERT: S 642 ARG cc_start: 0.7930 (ptp-110) cc_final: 0.7622 (ptp-110) outliers start: 139 outliers final: 52 residues processed: 1019 average time/residue: 1.5907 time to fit residues: 1929.7461 Evaluate side-chains 998 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 923 time to evaluate : 4.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 207 LYS Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 190 LYS Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 590 LEU Chi-restraints excluded: chain R residue 734 LYS Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 323 GLU Chi-restraints excluded: chain Q residue 539 LYS Chi-restraints excluded: chain P residue 373 GLU Chi-restraints excluded: chain P residue 791 LEU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 591 PHE Chi-restraints excluded: chain O residue 719 LEU Chi-restraints excluded: chain O residue 755 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain O residue 797 VAL Chi-restraints excluded: chain T residue 170 PHE Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 244 TYR Chi-restraints excluded: chain T residue 337 ARG Chi-restraints excluded: chain T residue 362 TYR Chi-restraints excluded: chain T residue 401 GLU Chi-restraints excluded: chain T residue 707 LEU Chi-restraints excluded: chain T residue 733 ASP Chi-restraints excluded: chain S residue 279 ILE Chi-restraints excluded: chain S residue 286 HIS Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 609 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 545 optimal weight: 0.4980 chunk 335 optimal weight: 5.9990 chunk 476 optimal weight: 0.9980 chunk 502 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 366 optimal weight: 2.9990 chunk 310 optimal weight: 0.9980 chunk 308 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN G 101 ASN J 122 GLN J 157 GLN K 222 GLN M 122 GLN N 156 HIS R 173 ASN R 198 GLN P 700 GLN ** T 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 ASN S 674 ASN S 700 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.113860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.088915 restraints weight = 78458.754| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.72 r_work: 0.3489 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 47905 Z= 0.175 Angle : 0.571 10.570 64729 Z= 0.285 Chirality : 0.042 0.214 7460 Planarity : 0.004 0.066 8401 Dihedral : 9.119 179.956 6859 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.89 % Favored : 95.99 % Rotamer: Outliers : 2.67 % Allowed : 18.34 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.11), residues: 5962 helix: 1.95 (0.09), residues: 3207 sheet: 0.53 (0.17), residues: 799 loop : -0.42 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 189 HIS 0.007 0.001 HIS O 286 PHE 0.022 0.001 PHE O 261 TYR 0.020 0.001 TYR H 159 ARG 0.016 0.000 ARG R 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 943 time to evaluate : 4.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.8630 (m-40) cc_final: 0.8312 (m110) REVERT: E 203 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: F 197 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: H 115 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: H 229 MET cc_start: 0.8056 (mpp) cc_final: 0.7732 (mpp) REVERT: I 56 LYS cc_start: 0.7681 (mttt) cc_final: 0.7461 (mtmt) REVERT: I 228 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8457 (mttm) REVERT: J 222 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8331 (pt0) REVERT: M 190 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8454 (tptm) REVERT: N 181 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7606 (ttm-80) REVERT: R 262 GLU cc_start: 0.8294 (mp0) cc_final: 0.8044 (mp0) REVERT: R 305 LYS cc_start: 0.8787 (mmmm) cc_final: 0.8505 (ttmm) REVERT: R 335 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: R 522 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8335 (mtmm) REVERT: R 734 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8543 (mtpt) REVERT: R 743 ASP cc_start: 0.8232 (t0) cc_final: 0.7946 (t0) REVERT: Q 697 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8210 (mm-30) REVERT: Q 733 ASP cc_start: 0.8548 (t0) cc_final: 0.8274 (t0) REVERT: P 240 ASP cc_start: 0.8230 (m-30) cc_final: 0.8012 (m-30) REVERT: P 494 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8747 (ttmt) REVERT: P 570 GLU cc_start: 0.7978 (tt0) cc_final: 0.7701 (tt0) REVERT: P 669 ILE cc_start: 0.5963 (OUTLIER) cc_final: 0.5473 (mp) REVERT: P 791 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7442 (mt) REVERT: O 234 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8243 (t) REVERT: O 263 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7937 (tm-30) REVERT: O 267 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8748 (ttmt) REVERT: O 298 ILE cc_start: 0.7570 (pt) cc_final: 0.7357 (mt) REVERT: O 307 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7579 (mtm) REVERT: O 325 ARG cc_start: 0.7926 (ptm-80) cc_final: 0.7647 (ptm-80) REVERT: O 329 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7678 (mt-10) REVERT: O 405 ARG cc_start: 0.8314 (tpt170) cc_final: 0.7961 (tpm170) REVERT: O 506 MET cc_start: 0.6135 (ttp) cc_final: 0.5228 (ptm) REVERT: O 602 GLU cc_start: 0.8269 (pm20) cc_final: 0.7959 (pm20) REVERT: O 759 LYS cc_start: 0.8325 (tppp) cc_final: 0.7986 (tptp) REVERT: O 775 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7225 (tm130) REVERT: O 787 LEU cc_start: 0.8165 (mm) cc_final: 0.7947 (mt) REVERT: T 170 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7294 (t80) REVERT: T 207 ASN cc_start: 0.8494 (m110) cc_final: 0.8136 (m110) REVERT: T 223 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: T 244 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6335 (t80) REVERT: T 271 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8314 (tm-30) REVERT: T 272 ILE cc_start: 0.8989 (pt) cc_final: 0.8595 (pp) REVERT: T 304 LEU cc_start: 0.8496 (mm) cc_final: 0.8071 (pp) REVERT: T 305 LYS cc_start: 0.7990 (tppt) cc_final: 0.7645 (tptp) REVERT: T 308 LEU cc_start: 0.7684 (mt) cc_final: 0.7470 (tp) REVERT: T 337 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6940 (mtt-85) REVERT: T 401 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: T 502 ARG cc_start: 0.7412 (mmm160) cc_final: 0.6989 (mmm160) REVERT: T 575 SER cc_start: 0.8648 (t) cc_final: 0.8346 (p) REVERT: T 613 LYS cc_start: 0.8061 (pttm) cc_final: 0.7639 (tptt) REVERT: T 619 LEU cc_start: 0.8742 (tp) cc_final: 0.8442 (tm) REVERT: T 642 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7659 (ptt90) REVERT: T 687 TYR cc_start: 0.7818 (t80) cc_final: 0.7523 (t80) REVERT: T 733 ASP cc_start: 0.8778 (t0) cc_final: 0.8341 (m-30) REVERT: T 740 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8449 (mptm) REVERT: S 184 ASP cc_start: 0.7321 (p0) cc_final: 0.7040 (p0) REVERT: S 205 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7744 (mtpp) REVERT: S 279 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7807 (tp) REVERT: S 307 MET cc_start: 0.8471 (mmm) cc_final: 0.7982 (mmm) REVERT: S 319 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7687 (t) REVERT: S 354 ILE cc_start: 0.8723 (mt) cc_final: 0.8431 (tt) REVERT: S 405 ARG cc_start: 0.7768 (tpm-80) cc_final: 0.7553 (tpm-80) REVERT: S 609 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8756 (mtmt) REVERT: S 635 LEU cc_start: 0.8773 (tp) cc_final: 0.8492 (tm) REVERT: S 642 ARG cc_start: 0.7896 (ptp-110) cc_final: 0.7603 (ptp-110) outliers start: 134 outliers final: 58 residues processed: 1015 average time/residue: 1.5920 time to fit residues: 1924.5117 Evaluate side-chains 1011 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 929 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 222 GLN Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 190 LYS Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain R residue 335 GLU Chi-restraints excluded: chain R residue 522 LYS Chi-restraints excluded: chain R residue 734 LYS Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 238 LEU Chi-restraints excluded: chain Q residue 323 GLU Chi-restraints excluded: chain Q residue 539 LYS Chi-restraints excluded: chain P residue 373 GLU Chi-restraints excluded: chain P residue 494 LYS Chi-restraints excluded: chain P residue 669 ILE Chi-restraints excluded: chain P residue 791 LEU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 591 PHE Chi-restraints excluded: chain O residue 719 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain O residue 797 VAL Chi-restraints excluded: chain T residue 170 PHE Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 244 TYR Chi-restraints excluded: chain T residue 337 ARG Chi-restraints excluded: chain T residue 401 GLU Chi-restraints excluded: chain T residue 698 LEU Chi-restraints excluded: chain T residue 707 LEU Chi-restraints excluded: chain T residue 740 LYS Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain S residue 279 ILE Chi-restraints excluded: chain S residue 286 HIS Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain S residue 609 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 196 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 421 optimal weight: 4.9990 chunk 305 optimal weight: 0.4980 chunk 590 optimal weight: 10.9990 chunk 285 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 519 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 446 optimal weight: 3.9990 chunk 576 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 38 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN J 122 GLN M 122 GLN N 156 HIS R 173 ASN R 198 GLN P 700 GLN P 775 GLN O 701 HIS ** T 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 ASN S 674 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.112468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.087375 restraints weight = 78581.465| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.73 r_work: 0.3461 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 47905 Z= 0.233 Angle : 0.600 12.714 64729 Z= 0.302 Chirality : 0.043 0.212 7460 Planarity : 0.004 0.069 8401 Dihedral : 9.091 178.321 6859 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 2.94 % Allowed : 18.82 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.11), residues: 5962 helix: 1.95 (0.09), residues: 3188 sheet: 0.55 (0.17), residues: 816 loop : -0.50 (0.15), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 189 HIS 0.007 0.001 HIS O 286 PHE 0.039 0.001 PHE S 281 TYR 0.019 0.001 TYR O 324 ARG 0.020 0.001 ARG S 709 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 939 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: H 115 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: H 229 MET cc_start: 0.8079 (mpp) cc_final: 0.7674 (mpp) REVERT: I 56 LYS cc_start: 0.7711 (mttt) cc_final: 0.7482 (mtmt) REVERT: I 228 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8477 (mttm) REVERT: J 222 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: M 64 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8530 (t80) REVERT: M 190 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8514 (tptm) REVERT: N 181 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7664 (ttm-80) REVERT: R 230 VAL cc_start: 0.8748 (t) cc_final: 0.8544 (p) REVERT: R 262 GLU cc_start: 0.8295 (mp0) cc_final: 0.8015 (mp0) REVERT: R 305 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8546 (ttmm) REVERT: R 335 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: R 522 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8379 (mtmm) REVERT: R 734 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8515 (mtpt) REVERT: R 743 ASP cc_start: 0.8295 (t0) cc_final: 0.7959 (t0) REVERT: Q 697 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8243 (mm-30) REVERT: Q 733 ASP cc_start: 0.8594 (t0) cc_final: 0.8321 (t0) REVERT: P 240 ASP cc_start: 0.8296 (m-30) cc_final: 0.8071 (m-30) REVERT: P 494 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8743 (ttmt) REVERT: P 570 GLU cc_start: 0.8021 (tt0) cc_final: 0.7756 (tt0) REVERT: P 791 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7610 (mt) REVERT: O 263 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7911 (tm-30) REVERT: O 267 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8744 (ttmt) REVERT: O 298 ILE cc_start: 0.7654 (pt) cc_final: 0.7439 (mt) REVERT: O 307 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7537 (mtm) REVERT: O 325 ARG cc_start: 0.7973 (ptm-80) cc_final: 0.7670 (ptm-80) REVERT: O 329 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7664 (mt-10) REVERT: O 405 ARG cc_start: 0.8372 (tpt170) cc_final: 0.8012 (tpm170) REVERT: O 407 ARG cc_start: 0.8797 (tpp80) cc_final: 0.8522 (tpp-160) REVERT: O 506 MET cc_start: 0.6368 (ttp) cc_final: 0.5424 (ptm) REVERT: O 564 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7226 (mm-30) REVERT: O 602 GLU cc_start: 0.8299 (pm20) cc_final: 0.8005 (pm20) REVERT: O 759 LYS cc_start: 0.8346 (tppp) cc_final: 0.8014 (tptp) REVERT: O 775 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7294 (tm130) REVERT: O 787 LEU cc_start: 0.8187 (mm) cc_final: 0.7959 (mt) REVERT: O 813 ARG cc_start: 0.5860 (ttp80) cc_final: 0.5278 (ttp80) REVERT: T 170 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7324 (t80) REVERT: T 207 ASN cc_start: 0.8528 (m110) cc_final: 0.8185 (m110) REVERT: T 223 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: T 244 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6324 (t80) REVERT: T 271 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8313 (tm-30) REVERT: T 272 ILE cc_start: 0.9001 (pt) cc_final: 0.8604 (pp) REVERT: T 304 LEU cc_start: 0.8521 (mm) cc_final: 0.8079 (pp) REVERT: T 308 LEU cc_start: 0.7731 (mt) cc_final: 0.6940 (tp) REVERT: T 337 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6856 (mtt-85) REVERT: T 401 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: T 575 SER cc_start: 0.8657 (t) cc_final: 0.8342 (p) REVERT: T 613 LYS cc_start: 0.8079 (pttm) cc_final: 0.7679 (tptt) REVERT: T 619 LEU cc_start: 0.8740 (tp) cc_final: 0.8441 (tm) REVERT: T 642 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7675 (ptt90) REVERT: T 643 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6064 (pp) REVERT: S 184 ASP cc_start: 0.7307 (p0) cc_final: 0.7039 (p0) REVERT: S 205 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7762 (mtpp) REVERT: S 218 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8214 (mttm) REVERT: S 279 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7838 (tp) REVERT: S 286 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6886 (p90) REVERT: S 307 MET cc_start: 0.8501 (mmm) cc_final: 0.8173 (mmm) REVERT: S 319 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7707 (t) REVERT: S 354 ILE cc_start: 0.8726 (mt) cc_final: 0.8440 (tt) REVERT: S 609 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8744 (mtmt) REVERT: S 635 LEU cc_start: 0.8780 (tp) cc_final: 0.8495 (tm) REVERT: S 639 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: S 642 ARG cc_start: 0.7930 (ptp-110) cc_final: 0.7626 (ptp-110) outliers start: 148 outliers final: 71 residues processed: 1010 average time/residue: 1.6378 time to fit residues: 1963.1587 Evaluate side-chains 1009 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 914 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 64 PHE Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain M residue 190 LYS Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain R residue 335 GLU Chi-restraints excluded: chain R residue 522 LYS Chi-restraints excluded: chain R residue 734 LYS Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 323 GLU Chi-restraints excluded: chain Q residue 570 GLU Chi-restraints excluded: chain P residue 373 GLU Chi-restraints excluded: chain P residue 494 LYS Chi-restraints excluded: chain P residue 791 LEU Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 577 ASP Chi-restraints excluded: chain O residue 591 PHE Chi-restraints excluded: chain O residue 719 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain O residue 797 VAL Chi-restraints excluded: chain T residue 170 PHE Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 244 TYR Chi-restraints excluded: chain T residue 337 ARG Chi-restraints excluded: chain T residue 401 GLU Chi-restraints excluded: chain T residue 643 LEU Chi-restraints excluded: chain T residue 698 LEU Chi-restraints excluded: chain T residue 707 LEU Chi-restraints excluded: chain S residue 279 ILE Chi-restraints excluded: chain S residue 286 HIS Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain S residue 609 LYS Chi-restraints excluded: chain S residue 639 GLU Chi-restraints excluded: chain S residue 710 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 538 optimal weight: 10.0000 chunk 389 optimal weight: 5.9990 chunk 390 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 368 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 371 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 38 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN J 115 GLN J 122 GLN J 183 GLN K 166 GLN K 222 GLN M 68 GLN N 156 HIS R 173 ASN R 198 GLN R 342 GLN P 700 GLN P 775 GLN O 701 HIS ** T 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 ASN S 674 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.111363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.086220 restraints weight = 78042.969| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.72 r_work: 0.3442 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 47905 Z= 0.278 Angle : 0.636 11.619 64729 Z= 0.321 Chirality : 0.044 0.210 7460 Planarity : 0.005 0.098 8401 Dihedral : 9.172 176.373 6859 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 2.79 % Allowed : 19.54 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.11), residues: 5962 helix: 1.84 (0.09), residues: 3192 sheet: 0.55 (0.17), residues: 820 loop : -0.58 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 189 HIS 0.007 0.001 HIS O 286 PHE 0.026 0.002 PHE O 261 TYR 0.023 0.002 TYR H 159 ARG 0.017 0.001 ARG R 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 941 time to evaluate : 4.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.8649 (m-40) cc_final: 0.8351 (m110) REVERT: H 115 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: H 229 MET cc_start: 0.8135 (mpp) cc_final: 0.7710 (mpp) REVERT: I 56 LYS cc_start: 0.7750 (mttt) cc_final: 0.7480 (mtmt) REVERT: I 228 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8611 (mttm) REVERT: J 222 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: M 64 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8505 (t80) REVERT: M 190 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8526 (tptm) REVERT: N 181 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7661 (ttm-80) REVERT: R 262 GLU cc_start: 0.8249 (mp0) cc_final: 0.7952 (mp0) REVERT: R 279 ILE cc_start: 0.9164 (tt) cc_final: 0.8958 (tp) REVERT: R 305 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8539 (ttmm) REVERT: R 325 ARG cc_start: 0.8387 (tmm-80) cc_final: 0.8122 (tmm-80) REVERT: R 335 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: R 743 ASP cc_start: 0.8298 (t0) cc_final: 0.7949 (t0) REVERT: Q 591 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8599 (m-80) REVERT: Q 697 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8249 (mm-30) REVERT: P 240 ASP cc_start: 0.8279 (m-30) cc_final: 0.8068 (m-30) REVERT: P 494 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8803 (ttmt) REVERT: P 570 GLU cc_start: 0.8011 (tt0) cc_final: 0.7758 (tt0) REVERT: P 791 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7858 (mt) REVERT: O 263 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7896 (tm-30) REVERT: O 267 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8760 (ttmt) REVERT: O 307 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7531 (mtm) REVERT: O 320 THR cc_start: 0.9022 (m) cc_final: 0.8758 (p) REVERT: O 325 ARG cc_start: 0.7950 (ptm-80) cc_final: 0.7690 (ptm-80) REVERT: O 329 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7697 (mt-10) REVERT: O 405 ARG cc_start: 0.8358 (tpt170) cc_final: 0.7994 (tpm170) REVERT: O 407 ARG cc_start: 0.8799 (tpp80) cc_final: 0.8454 (tpp-160) REVERT: O 506 MET cc_start: 0.6346 (ttp) cc_final: 0.5409 (ptm) REVERT: O 602 GLU cc_start: 0.8342 (pm20) cc_final: 0.8053 (pm20) REVERT: O 696 ASP cc_start: 0.8104 (m-30) cc_final: 0.7608 (m-30) REVERT: O 744 MET cc_start: 0.7823 (tmm) cc_final: 0.7526 (tpp) REVERT: O 759 LYS cc_start: 0.8339 (tppp) cc_final: 0.8023 (tptp) REVERT: O 775 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7366 (tm130) REVERT: O 787 LEU cc_start: 0.8212 (mm) cc_final: 0.7971 (mt) REVERT: O 813 ARG cc_start: 0.5927 (ttp80) cc_final: 0.5496 (ttp80) REVERT: T 170 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7308 (t80) REVERT: T 207 ASN cc_start: 0.8534 (m110) cc_final: 0.8175 (m110) REVERT: T 223 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: T 233 GLU cc_start: 0.8443 (mp0) cc_final: 0.8181 (mp0) REVERT: T 244 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6358 (t80) REVERT: T 271 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8293 (tm-30) REVERT: T 272 ILE cc_start: 0.8988 (pt) cc_final: 0.8588 (pp) REVERT: T 283 ASP cc_start: 0.7806 (t0) cc_final: 0.7174 (OUTLIER) REVERT: T 304 LEU cc_start: 0.8529 (mm) cc_final: 0.8111 (pp) REVERT: T 308 LEU cc_start: 0.7673 (mt) cc_final: 0.7408 (tp) REVERT: T 337 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7017 (mtt-85) REVERT: T 401 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: T 502 ARG cc_start: 0.7414 (mmm160) cc_final: 0.6975 (mmm160) REVERT: T 575 SER cc_start: 0.8666 (t) cc_final: 0.8337 (p) REVERT: T 619 LEU cc_start: 0.8727 (tp) cc_final: 0.8429 (tm) REVERT: T 643 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6773 (mt) REVERT: T 734 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8600 (mppt) REVERT: T 744 MET cc_start: 0.7132 (mmt) cc_final: 0.6926 (mmm) REVERT: S 184 ASP cc_start: 0.7235 (p0) cc_final: 0.6974 (p0) REVERT: S 205 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7800 (mtpp) REVERT: S 218 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8093 (mtpp) REVERT: S 267 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8695 (pttm) REVERT: S 307 MET cc_start: 0.8290 (mmm) cc_final: 0.8043 (mmm) REVERT: S 315 THR cc_start: 0.8552 (p) cc_final: 0.8191 (t) REVERT: S 319 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7862 (t) REVERT: S 609 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8725 (mtmt) REVERT: S 635 LEU cc_start: 0.8769 (tp) cc_final: 0.7945 (tm) REVERT: S 642 ARG cc_start: 0.7884 (ptp-110) cc_final: 0.7610 (ptp-110) outliers start: 140 outliers final: 78 residues processed: 1016 average time/residue: 1.6158 time to fit residues: 1950.2972 Evaluate side-chains 1024 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 927 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain J residue 226 THR Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 64 PHE Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain M residue 190 LYS Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain R residue 335 GLU Chi-restraints excluded: chain R residue 475 VAL Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 209 VAL Chi-restraints excluded: chain Q residue 323 GLU Chi-restraints excluded: chain Q residue 373 GLU Chi-restraints excluded: chain Q residue 570 GLU Chi-restraints excluded: chain Q residue 591 PHE Chi-restraints excluded: chain P residue 237 THR Chi-restraints excluded: chain P residue 373 GLU Chi-restraints excluded: chain P residue 494 LYS Chi-restraints excluded: chain P residue 791 LEU Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 577 ASP Chi-restraints excluded: chain O residue 591 PHE Chi-restraints excluded: chain O residue 719 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain O residue 797 VAL Chi-restraints excluded: chain T residue 170 PHE Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 244 TYR Chi-restraints excluded: chain T residue 315 THR Chi-restraints excluded: chain T residue 337 ARG Chi-restraints excluded: chain T residue 401 GLU Chi-restraints excluded: chain T residue 643 LEU Chi-restraints excluded: chain T residue 698 LEU Chi-restraints excluded: chain T residue 707 LEU Chi-restraints excluded: chain T residue 734 LYS Chi-restraints excluded: chain T residue 764 VAL Chi-restraints excluded: chain S residue 286 HIS Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain S residue 609 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 514 optimal weight: 20.0000 chunk 398 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 491 optimal weight: 0.0870 chunk 111 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 chunk 411 optimal weight: 2.9990 chunk 526 optimal weight: 9.9990 chunk 336 optimal weight: 0.8980 chunk 290 optimal weight: 0.8980 chunk 573 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 38 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 128 GLN J 122 GLN K 166 GLN K 222 GLN M 122 GLN N 156 HIS R 173 ASN R 198 GLN R 342 GLN P 700 GLN P 775 GLN ** T 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 674 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.112871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.087751 restraints weight = 78428.720| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.73 r_work: 0.3469 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 47905 Z= 0.200 Angle : 0.625 13.134 64729 Z= 0.314 Chirality : 0.042 0.207 7460 Planarity : 0.004 0.092 8401 Dihedral : 9.006 174.851 6859 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.89 % Favored : 95.99 % Rotamer: Outliers : 2.31 % Allowed : 20.67 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.11), residues: 5962 helix: 1.91 (0.09), residues: 3181 sheet: 0.56 (0.17), residues: 819 loop : -0.54 (0.15), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 189 HIS 0.008 0.001 HIS O 286 PHE 0.025 0.001 PHE O 261 TYR 0.021 0.001 TYR O 324 ARG 0.015 0.001 ARG S 540 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 934 time to evaluate : 4.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.8658 (m-40) cc_final: 0.8341 (m110) REVERT: F 39 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8266 (ttp80) REVERT: F 197 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: H 115 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8100 (mp10) REVERT: H 229 MET cc_start: 0.8141 (mpp) cc_final: 0.7722 (mpp) REVERT: I 56 LYS cc_start: 0.7718 (mttt) cc_final: 0.7463 (mtmt) REVERT: I 228 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8755 (mttm) REVERT: J 222 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8413 (pt0) REVERT: M 64 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8532 (t80) REVERT: M 190 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8485 (tptm) REVERT: N 181 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7656 (ttm-80) REVERT: R 262 GLU cc_start: 0.8203 (mp0) cc_final: 0.7985 (mp0) REVERT: R 279 ILE cc_start: 0.9134 (tt) cc_final: 0.8926 (tp) REVERT: R 305 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8492 (ttmm) REVERT: R 522 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8365 (mtmm) REVERT: R 743 ASP cc_start: 0.8306 (t0) cc_final: 0.7957 (t0) REVERT: Q 591 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: Q 697 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8247 (mm-30) REVERT: P 240 ASP cc_start: 0.8278 (m-30) cc_final: 0.8067 (m-30) REVERT: P 494 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8817 (ttmt) REVERT: P 570 GLU cc_start: 0.8009 (tt0) cc_final: 0.7760 (tt0) REVERT: P 669 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5710 (mm) REVERT: P 791 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7795 (mt) REVERT: O 263 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7886 (tm-30) REVERT: O 267 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8756 (ttmt) REVERT: O 307 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7510 (mtm) REVERT: O 325 ARG cc_start: 0.7944 (ptm-80) cc_final: 0.7667 (ptm-80) REVERT: O 329 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7698 (mt-10) REVERT: O 405 ARG cc_start: 0.8378 (tpt170) cc_final: 0.8024 (tpm170) REVERT: O 407 ARG cc_start: 0.8764 (tpp80) cc_final: 0.8427 (tpp-160) REVERT: O 530 ARG cc_start: 0.8014 (ttp-110) cc_final: 0.7813 (ttp-110) REVERT: O 602 GLU cc_start: 0.8300 (pm20) cc_final: 0.8016 (pm20) REVERT: O 744 MET cc_start: 0.7808 (tmm) cc_final: 0.7544 (tpp) REVERT: O 759 LYS cc_start: 0.8344 (tppp) cc_final: 0.8036 (tptp) REVERT: O 770 LEU cc_start: 0.8980 (tp) cc_final: 0.8657 (tm) REVERT: O 775 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7326 (tm130) REVERT: O 787 LEU cc_start: 0.8198 (mm) cc_final: 0.7963 (mt) REVERT: O 800 ASP cc_start: 0.6711 (t70) cc_final: 0.6362 (t70) REVERT: O 813 ARG cc_start: 0.5869 (ttp80) cc_final: 0.5489 (ttp80) REVERT: T 170 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7347 (t80) REVERT: T 207 ASN cc_start: 0.8521 (m110) cc_final: 0.8175 (m110) REVERT: T 223 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: T 244 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6276 (t80) REVERT: T 271 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8313 (tm-30) REVERT: T 272 ILE cc_start: 0.9023 (pt) cc_final: 0.8714 (pp) REVERT: T 283 ASP cc_start: 0.7808 (t0) cc_final: 0.7154 (OUTLIER) REVERT: T 304 LEU cc_start: 0.8539 (mm) cc_final: 0.8090 (pp) REVERT: T 305 LYS cc_start: 0.8402 (mmmm) cc_final: 0.7724 (tppt) REVERT: T 401 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: T 483 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8017 (p) REVERT: T 502 ARG cc_start: 0.7401 (mmm160) cc_final: 0.6988 (mmm160) REVERT: T 575 SER cc_start: 0.8657 (t) cc_final: 0.8352 (p) REVERT: T 619 LEU cc_start: 0.8709 (tp) cc_final: 0.8419 (tm) REVERT: T 642 ARG cc_start: 0.7547 (pmm-80) cc_final: 0.7230 (pmm-80) REVERT: T 643 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6715 (mt) REVERT: T 687 TYR cc_start: 0.7826 (t80) cc_final: 0.7517 (t80) REVERT: T 734 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8559 (mppt) REVERT: T 742 ARG cc_start: 0.8405 (tmt-80) cc_final: 0.8090 (tpt-90) REVERT: S 184 ASP cc_start: 0.7235 (p0) cc_final: 0.7010 (p0) REVERT: S 205 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7754 (mtpm) REVERT: S 279 ILE cc_start: 0.8362 (mm) cc_final: 0.7996 (mp) REVERT: S 286 HIS cc_start: 0.7341 (OUTLIER) cc_final: 0.6804 (p90) REVERT: S 315 THR cc_start: 0.8493 (p) cc_final: 0.8107 (t) REVERT: S 316 ILE cc_start: 0.8669 (mp) cc_final: 0.8307 (mp) REVERT: S 319 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7936 (t) REVERT: S 335 GLU cc_start: 0.7680 (pp20) cc_final: 0.7339 (pt0) REVERT: S 405 ARG cc_start: 0.7823 (tpm-80) cc_final: 0.7585 (tpm-80) REVERT: S 506 MET cc_start: 0.8601 (ttt) cc_final: 0.8348 (ttm) REVERT: S 609 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8719 (mtmt) REVERT: S 642 ARG cc_start: 0.7898 (ptp-110) cc_final: 0.7622 (ptp-110) REVERT: S 692 ASN cc_start: 0.8102 (m110) cc_final: 0.7793 (m110) outliers start: 116 outliers final: 67 residues processed: 994 average time/residue: 1.6586 time to fit residues: 1953.3099 Evaluate side-chains 1011 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 922 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 198 LYS Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 64 PHE Chi-restraints excluded: chain M residue 190 LYS Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain R residue 522 LYS Chi-restraints excluded: chain R residue 696 ASP Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain R residue 791 LEU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 209 VAL Chi-restraints excluded: chain Q residue 323 GLU Chi-restraints excluded: chain Q residue 570 GLU Chi-restraints excluded: chain Q residue 591 PHE Chi-restraints excluded: chain P residue 373 GLU Chi-restraints excluded: chain P residue 494 LYS Chi-restraints excluded: chain P residue 669 ILE Chi-restraints excluded: chain P residue 783 SER Chi-restraints excluded: chain P residue 791 LEU Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 591 PHE Chi-restraints excluded: chain O residue 719 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain O residue 797 VAL Chi-restraints excluded: chain T residue 170 PHE Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 244 TYR Chi-restraints excluded: chain T residue 366 HIS Chi-restraints excluded: chain T residue 401 GLU Chi-restraints excluded: chain T residue 483 VAL Chi-restraints excluded: chain T residue 643 LEU Chi-restraints excluded: chain T residue 698 LEU Chi-restraints excluded: chain T residue 707 LEU Chi-restraints excluded: chain T residue 734 LYS Chi-restraints excluded: chain T residue 764 VAL Chi-restraints excluded: chain S residue 286 HIS Chi-restraints excluded: chain S residue 319 THR Chi-restraints excluded: chain S residue 609 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 388 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 270 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 271 optimal weight: 0.4980 chunk 357 optimal weight: 3.9990 chunk 494 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 323 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 38 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 183 GLN J 122 GLN J 150 ASN K 166 GLN M 122 GLN N 156 HIS R 173 ASN R 206 ASN R 342 GLN P 700 GLN P 775 GLN O 198 GLN O 701 HIS ** T 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 ASN S 674 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.113499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.088512 restraints weight = 78233.383| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.73 r_work: 0.3481 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 47905 Z= 0.188 Angle : 0.628 11.930 64729 Z= 0.314 Chirality : 0.042 0.233 7460 Planarity : 0.004 0.077 8401 Dihedral : 8.856 176.050 6859 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.91 % Rotamer: Outliers : 1.95 % Allowed : 21.61 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.11), residues: 5962 helix: 1.90 (0.09), residues: 3192 sheet: 0.66 (0.17), residues: 812 loop : -0.51 (0.15), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 189 HIS 0.008 0.001 HIS T 350 PHE 0.025 0.001 PHE O 261 TYR 0.022 0.001 TYR H 159 ARG 0.026 0.001 ARG T 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11924 Ramachandran restraints generated. 5962 Oldfield, 0 Emsley, 5962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 949 time to evaluate : 4.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ASN cc_start: 0.8613 (m-40) cc_final: 0.8313 (m110) REVERT: F 39 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8231 (ttp80) REVERT: H 115 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: H 229 MET cc_start: 0.8110 (mpp) cc_final: 0.7703 (mpp) REVERT: I 56 LYS cc_start: 0.7722 (mttt) cc_final: 0.7490 (mtmt) REVERT: I 228 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8647 (mttm) REVERT: J 222 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: M 64 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8501 (t80) REVERT: M 179 ARG cc_start: 0.8782 (ttp-110) cc_final: 0.8484 (ttp-110) REVERT: M 190 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8438 (tptm) REVERT: N 181 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7630 (ttm-80) REVERT: R 279 ILE cc_start: 0.9110 (tt) cc_final: 0.8908 (tp) REVERT: R 522 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: R 743 ASP cc_start: 0.8265 (t0) cc_final: 0.7942 (t0) REVERT: Q 591 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: Q 697 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8218 (mm-30) REVERT: P 240 ASP cc_start: 0.8225 (m-30) cc_final: 0.8024 (m-30) REVERT: P 494 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8786 (ttmt) REVERT: P 570 GLU cc_start: 0.7942 (tt0) cc_final: 0.7719 (tt0) REVERT: P 669 ILE cc_start: 0.6190 (OUTLIER) cc_final: 0.5763 (mm) REVERT: P 775 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8173 (tp40) REVERT: P 791 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7775 (mt) REVERT: P 796 ILE cc_start: 0.8893 (mm) cc_final: 0.8524 (tt) REVERT: O 263 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7842 (tm-30) REVERT: O 267 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8749 (ttmt) REVERT: O 298 ILE cc_start: 0.7645 (pt) cc_final: 0.7418 (mt) REVERT: O 307 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7569 (mtm) REVERT: O 325 ARG cc_start: 0.7909 (ptm-80) cc_final: 0.7673 (ptm-80) REVERT: O 329 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7732 (mt-10) REVERT: O 405 ARG cc_start: 0.8325 (tpt170) cc_final: 0.7988 (tpm170) REVERT: O 407 ARG cc_start: 0.8744 (tpp80) cc_final: 0.8432 (tpp-160) REVERT: O 509 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7509 (mp0) REVERT: O 602 GLU cc_start: 0.8253 (pm20) cc_final: 0.7990 (pm20) REVERT: O 744 MET cc_start: 0.7810 (tmm) cc_final: 0.7594 (tpp) REVERT: O 759 LYS cc_start: 0.8316 (tppp) cc_final: 0.8019 (tptp) REVERT: O 770 LEU cc_start: 0.8984 (tp) cc_final: 0.8668 (tm) REVERT: O 775 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7306 (tm130) REVERT: O 787 LEU cc_start: 0.8186 (mm) cc_final: 0.7961 (mt) REVERT: O 800 ASP cc_start: 0.6710 (t70) cc_final: 0.6373 (t70) REVERT: O 813 ARG cc_start: 0.5880 (ttp80) cc_final: 0.5406 (ttp80) REVERT: T 170 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7294 (t80) REVERT: T 207 ASN cc_start: 0.8542 (m110) cc_final: 0.8219 (m110) REVERT: T 223 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: T 233 GLU cc_start: 0.8420 (mp0) cc_final: 0.8215 (mp0) REVERT: T 244 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.6292 (t80) REVERT: T 271 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8311 (tm-30) REVERT: T 272 ILE cc_start: 0.9075 (pt) cc_final: 0.8873 (pp) REVERT: T 283 ASP cc_start: 0.7801 (t0) cc_final: 0.7170 (OUTLIER) REVERT: T 304 LEU cc_start: 0.8574 (mm) cc_final: 0.8117 (pp) REVERT: T 337 ARG cc_start: 0.6926 (mpt-90) cc_final: 0.6712 (mtt-85) REVERT: T 401 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: T 483 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8057 (p) REVERT: T 502 ARG cc_start: 0.7394 (mmm160) cc_final: 0.6986 (mmm160) REVERT: T 613 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7617 (pmtt) REVERT: T 619 LEU cc_start: 0.8740 (tp) cc_final: 0.8444 (tm) REVERT: T 643 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6697 (mt) REVERT: T 687 TYR cc_start: 0.7780 (t80) cc_final: 0.7453 (t80) REVERT: S 184 ASP cc_start: 0.7213 (p0) cc_final: 0.6999 (p0) REVERT: S 279 ILE cc_start: 0.8401 (mm) cc_final: 0.8045 (mp) REVERT: S 286 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6780 (p90) REVERT: S 304 LEU cc_start: 0.8912 (mm) cc_final: 0.8664 (tm) REVERT: S 315 THR cc_start: 0.8473 (p) cc_final: 0.8063 (t) REVERT: S 316 ILE cc_start: 0.8712 (mp) cc_final: 0.8346 (mp) REVERT: S 319 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7895 (t) REVERT: S 335 GLU cc_start: 0.7667 (pp20) cc_final: 0.7363 (pt0) REVERT: S 506 MET cc_start: 0.8590 (ttt) cc_final: 0.8358 (ttm) REVERT: S 540 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7565 (mtp-110) REVERT: S 642 ARG cc_start: 0.7859 (ptp-110) cc_final: 0.7597 (ptp-110) REVERT: S 692 ASN cc_start: 0.8047 (m110) cc_final: 0.7743 (m110) outliers start: 98 outliers final: 60 residues processed: 997 average time/residue: 1.6261 time to fit residues: 1927.5902 Evaluate side-chains 1002 residues out of total 5027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 922 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 64 PHE Chi-restraints excluded: chain M residue 190 LYS Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 181 ARG Chi-restraints excluded: chain R residue 522 LYS Chi-restraints excluded: chain R residue 748 LEU Chi-restraints excluded: chain Q residue 204 THR Chi-restraints excluded: chain Q residue 209 VAL Chi-restraints excluded: chain Q residue 323 GLU Chi-restraints excluded: chain Q residue 570 GLU Chi-restraints excluded: chain Q residue 591 PHE Chi-restraints excluded: chain P residue 373 GLU Chi-restraints excluded: chain P residue 494 LYS Chi-restraints excluded: chain P residue 669 ILE Chi-restraints excluded: chain P residue 775 GLN Chi-restraints excluded: chain P residue 783 SER Chi-restraints excluded: chain P residue 791 LEU Chi-restraints excluded: chain O residue 307 MET Chi-restraints excluded: chain O residue 577 ASP Chi-restraints excluded: chain O residue 591 PHE Chi-restraints excluded: chain O residue 715 VAL Chi-restraints excluded: chain O residue 719 LEU Chi-restraints excluded: chain O residue 764 VAL Chi-restraints excluded: chain O residue 797 VAL Chi-restraints excluded: chain T residue 170 PHE Chi-restraints excluded: chain T residue 223 GLU Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 244 TYR Chi-restraints excluded: chain T residue 315 THR Chi-restraints excluded: chain T residue 401 GLU Chi-restraints excluded: chain T residue 483 VAL Chi-restraints excluded: chain T residue 643 LEU Chi-restraints excluded: chain T residue 698 LEU Chi-restraints excluded: chain T residue 707 LEU Chi-restraints excluded: chain T residue 764 VAL Chi-restraints excluded: chain S residue 286 HIS Chi-restraints excluded: chain S residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 592 random chunks: chunk 71 optimal weight: 0.9980 chunk 397 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 327 optimal weight: 0.9990 chunk 536 optimal weight: 9.9990 chunk 104 optimal weight: 0.0770 chunk 154 optimal weight: 0.0980 chunk 195 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN B 38 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 GLN J 115 GLN J 122 GLN N 156 HIS R 173 ASN R 198 GLN R 342 GLN R 718 GLN P 700 GLN O 198 GLN T 795 HIS S 207 ASN S 674 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.114074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.089166 restraints weight = 78097.911| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.72 r_work: 0.3493 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 47905 Z= 0.185 Angle : 0.634 12.793 64729 Z= 0.316 Chirality : 0.042 0.209 7460 Planarity : 0.004 0.064 8401 Dihedral : 8.708 177.752 6859 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 1.87 % Allowed : 22.05 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.11), residues: 5962 helix: 1.93 (0.09), residues: 3194 sheet: 0.65 (0.17), residues: 824 loop : -0.45 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 189 HIS 0.009 0.001 HIS T 350 PHE 0.026 0.001 PHE O 261 TYR 0.020 0.001 TYR O 324 ARG 0.015 0.001 ARG S 709 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 65394.41 seconds wall clock time: 1107 minutes 45.75 seconds (66465.75 seconds total)