Starting phenix.real_space_refine on Mon Oct 14 17:14:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/10_2024/8kg6_37211.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/10_2024/8kg6_37211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/10_2024/8kg6_37211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/10_2024/8kg6_37211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/10_2024/8kg6_37211.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg6_37211/10_2024/8kg6_37211.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.062 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: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 70 5.49 5 Mg 5 5.21 5 S 310 5.16 5 C 44722 2.51 5 N 12061 2.21 5 O 13438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 70613 Number of models: 1 Model: "" Number of chains: 27 Chain: "2" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5245 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 636} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5005 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 29, 'TRANS': 615} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "4" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5494 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 23, 'TRANS': 672} Chain breaks: 5 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "5" Number of atoms: 5334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5334 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 26, 'TRANS': 650} Chain breaks: 6 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "6" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4880 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 596} Chain breaks: 6 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "7" Number of atoms: 5023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5023 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 30, 'TRANS': 616} Chain breaks: 6 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1625 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1630 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain breaks: 1 Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1394 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2004 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 2 Chain: "E" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4591 Classifications: {'peptide': 568} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 552} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3467 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3362 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3358 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 722 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 438 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "K" Number of atoms: 5350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5350 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 639} Chain breaks: 7 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 788 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "M" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6490 Classifications: {'peptide': 813} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 29, 'TRANS': 783} Chain breaks: 6 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "N" Number of atoms: 4254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4254 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 30, 'TRANS': 505} Chain breaks: 5 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1311 SG CYS 2 341 91.897 160.539 137.536 1.00153.63 S ATOM 1334 SG CYS 2 344 92.545 163.894 138.191 1.00159.01 S ATOM 1492 SG CYS 2 364 95.627 160.829 138.766 1.00160.53 S ATOM 11648 SG CYS 4 349 104.539 156.837 175.423 1.00186.60 S ATOM 11669 SG CYS 4 352 107.704 157.643 177.327 1.00202.71 S ATOM 11816 SG CYS 4 371 104.315 158.571 178.805 1.00219.14 S ATOM 11858 SG CYS 4 376 105.748 160.465 175.846 1.00235.75 S ATOM 16884 SG CYS 5 183 67.104 160.118 139.094 1.00107.24 S ATOM 16909 SG CYS 5 186 65.273 163.289 138.503 1.00112.73 S ATOM 17073 SG CYS 5 211 68.943 163.526 138.513 1.00112.92 S ATOM 17110 SG CYS 5 236 67.373 162.812 141.804 1.00122.35 S ATOM 22306 SG CYS 6 311 108.480 157.777 152.137 1.00161.60 S ATOM 22328 SG CYS 6 314 109.321 161.325 151.410 1.00168.39 S ATOM 22485 SG CYS 6 333 108.706 160.246 155.063 1.00189.41 S ATOM 22519 SG CYS 6 338 105.844 160.521 152.596 1.00185.49 S ATOM 27551 SG CYS 7 262 76.725 156.156 183.223 1.00202.99 S ATOM 27724 SG CYS 7 284 74.839 158.131 182.583 1.00221.60 S ATOM 27761 SG CYS 7 289 76.704 160.520 182.003 1.00254.18 S ATOM 65286 SG CYS M2108 96.942 48.673 69.063 1.00120.64 S ATOM 65313 SG CYS M2111 98.826 46.173 71.235 1.00122.53 S ATOM 65462 SG CYS M2130 99.694 49.751 71.447 1.00114.26 S ATOM 65486 SG CYS M2133 100.623 47.823 68.309 1.00116.36 S ATOM 65749 SG CYS M2164 75.763 77.695 100.085 1.00 73.50 S ATOM 65772 SG CYS M2167 75.485 75.026 102.819 1.00 75.91 S ATOM 65873 SG CYS M2179 72.342 76.306 101.102 1.00 69.00 S ATOM 65886 SG CYS M2181 74.362 78.530 103.451 1.00 67.20 S Time building chain proxies: 30.49, per 1000 atoms: 0.43 Number of scatterers: 70613 At special positions: 0 Unit cell: (173.84, 244.86, 231.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 310 16.00 P 70 15.00 Mg 5 11.99 O 13438 8.00 N 12061 7.00 C 44722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.27 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 364 " pdb=" ZN 41400 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 349 " pdb=" ZN 5 801 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 211 " pdb=" ZN 61101 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 289 " pdb=" ZN M3001 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2111 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2130 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2133 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2108 " pdb=" ZN M3002 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2181 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2164 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2167 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2179 " Number of angles added : 30 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16596 Finding SS restraints... Secondary structure from input PDB file: 328 helices and 81 sheets defined 47.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.57 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 removed outlier: 3.554A pdb=" N LEU 2 186 " --> pdb=" O THR 2 182 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 Processing helix chain '2' and resid 200 through 218 Processing helix chain '2' and resid 225 through 237 removed outlier: 3.560A pdb=" N ALA 2 229 " --> pdb=" O SER 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 252 Processing helix chain '2' and resid 253 through 263 Processing helix chain '2' and resid 263 through 283 removed outlier: 3.538A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 289 removed outlier: 3.645A pdb=" N ARG 2 288 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 Processing helix chain '2' and resid 435 through 443 Processing helix chain '2' and resid 477 through 489 removed outlier: 3.620A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 500 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 removed outlier: 3.703A pdb=" N ILE 2 552 " --> pdb=" O ALA 2 548 " (cutoff:3.500A) Processing helix chain '2' and resid 572 through 577 removed outlier: 3.540A pdb=" N THR 2 577 " --> pdb=" O ALA 2 573 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 609 through 612 Processing helix chain '2' and resid 613 through 618 Processing helix chain '2' and resid 620 through 626 Processing helix chain '2' and resid 652 through 656 removed outlier: 4.154A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 666 Processing helix chain '2' and resid 670 through 675 Processing helix chain '2' and resid 688 through 706 Processing helix chain '2' and resid 739 through 756 removed outlier: 3.862A pdb=" N GLU 2 754 " --> pdb=" O LYS 2 750 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE 2 755 " --> pdb=" O LYS 2 751 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 774 removed outlier: 4.009A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 782 through 799 removed outlier: 3.569A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER 2 799 " --> pdb=" O ARG 2 795 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 3.595A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 848 removed outlier: 3.611A pdb=" N ALA 2 837 " --> pdb=" O ASP 2 833 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) Processing helix chain '2' and resid 850 through 862 removed outlier: 4.620A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) Processing helix chain '2' and resid 863 through 865 No H-bonds generated for 'chain '2' and resid 863 through 865' Processing helix chain '3' and resid 19 through 35 Processing helix chain '3' and resid 35 through 55 removed outlier: 4.324A pdb=" N ARG 3 39 " --> pdb=" O PHE 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 107 Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 117 through 136 removed outlier: 3.536A pdb=" N PHE 3 121 " --> pdb=" O GLU 3 117 " (cutoff:3.500A) Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 161 through 163 No H-bonds generated for 'chain '3' and resid 161 through 163' Processing helix chain '3' and resid 172 through 176 removed outlier: 3.501A pdb=" N HIS 3 175 " --> pdb=" O THR 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 261 through 265 Processing helix chain '3' and resid 279 through 283 Processing helix chain '3' and resid 343 through 355 removed outlier: 3.639A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 366 Processing helix chain '3' and resid 374 through 386 Processing helix chain '3' and resid 414 through 426 removed outlier: 3.687A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 443 Processing helix chain '3' and resid 474 through 478 Processing helix chain '3' and resid 479 through 482 Processing helix chain '3' and resid 483 through 493 Processing helix chain '3' and resid 536 through 541 Processing helix chain '3' and resid 555 through 570 Processing helix chain '3' and resid 652 through 667 Processing helix chain '3' and resid 672 through 688 removed outlier: 3.781A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 690 through 694 removed outlier: 4.304A pdb=" N LYS 3 694 " --> pdb=" O ASN 3 691 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 716 removed outlier: 3.813A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 186 through 199 removed outlier: 3.535A pdb=" N CYS 4 190 " --> pdb=" O SER 4 186 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET 4 199 " --> pdb=" O ARG 4 195 " (cutoff:3.500A) Processing helix chain '4' and resid 202 through 210 removed outlier: 4.132A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 245 through 251 removed outlier: 3.809A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 Processing helix chain '4' and resid 264 through 288 Processing helix chain '4' and resid 292 through 299 Processing helix chain '4' and resid 313 through 317 removed outlier: 3.594A pdb=" N LEU 4 317 " --> pdb=" O MET 4 314 " (cutoff:3.500A) Processing helix chain '4' and resid 386 through 389 Processing helix chain '4' and resid 502 through 514 Processing helix chain '4' and resid 517 through 527 removed outlier: 3.968A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 572 through 585 removed outlier: 4.628A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 609 through 612 Processing helix chain '4' and resid 633 through 637 removed outlier: 3.789A pdb=" N MET 4 637 " --> pdb=" O PHE 4 634 " (cutoff:3.500A) Processing helix chain '4' and resid 638 through 652 Processing helix chain '4' and resid 687 through 693 removed outlier: 3.600A pdb=" N ASP 4 693 " --> pdb=" O THR 4 689 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 700 Processing helix chain '4' and resid 713 through 731 removed outlier: 3.772A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP 4 731 " --> pdb=" O LEU 4 727 " (cutoff:3.500A) Processing helix chain '4' and resid 746 through 758 removed outlier: 4.190A pdb=" N SER 4 752 " --> pdb=" O THR 4 748 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 780 Processing helix chain '4' and resid 794 through 811 removed outlier: 3.516A pdb=" N GLU 4 806 " --> pdb=" O ILE 4 802 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 837 removed outlier: 3.841A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN 4 823 " --> pdb=" O LEU 4 819 " (cutoff:3.500A) Processing helix chain '4' and resid 851 through 874 removed outlier: 4.489A pdb=" N ILE 4 857 " --> pdb=" O GLY 4 853 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN 4 858 " --> pdb=" O LYS 4 854 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU 4 863 " --> pdb=" O ARG 4 859 " (cutoff:3.500A) Processing helix chain '4' and resid 882 through 889 removed outlier: 3.790A pdb=" N LEU 4 886 " --> pdb=" O SER 4 882 " (cutoff:3.500A) Processing helix chain '4' and resid 899 through 913 removed outlier: 4.232A pdb=" N ILE 4 903 " --> pdb=" O GLU 4 899 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN 4 904 " --> pdb=" O SER 4 900 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG 4 909 " --> pdb=" O GLU 4 905 " (cutoff:3.500A) Processing helix chain '5' and resid 21 through 38 Processing helix chain '5' and resid 44 through 56 Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 72 through 82 removed outlier: 3.550A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 103 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 147 through 151 removed outlier: 3.704A pdb=" N LEU 5 151 " --> pdb=" O LEU 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 279 through 283 Processing helix chain '5' and resid 350 through 362 Processing helix chain '5' and resid 365 through 373 Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 Processing helix chain '5' and resid 445 through 450 Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 481 through 485 Processing helix chain '5' and resid 486 through 491 removed outlier: 3.785A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) Processing helix chain '5' and resid 492 through 499 removed outlier: 4.354A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 540 removed outlier: 3.744A pdb=" N ILE 5 540 " --> pdb=" O PRO 5 536 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 550 removed outlier: 3.778A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) Processing helix chain '5' and resid 561 through 577 Processing helix chain '5' and resid 578 through 591 removed outlier: 4.019A pdb=" N ALA 5 582 " --> pdb=" O GLY 5 578 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 removed outlier: 3.799A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 641 Processing helix chain '5' and resid 649 through 667 removed outlier: 3.868A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 693 removed outlier: 3.557A pdb=" N VAL 5 677 " --> pdb=" O GLN 5 673 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) Processing helix chain '5' and resid 708 through 722 Processing helix chain '5' and resid 730 through 737 Processing helix chain '5' and resid 749 through 758 removed outlier: 4.312A pdb=" N TYR 5 753 " --> pdb=" O ASP 5 749 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 122 Processing helix chain '6' and resid 134 through 147 Processing helix chain '6' and resid 155 through 161 Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 364 through 368 Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 406 through 411 removed outlier: 3.623A pdb=" N LEU 6 410 " --> pdb=" O ASP 6 406 " (cutoff:3.500A) Processing helix chain '6' and resid 500 through 507 Processing helix chain '6' and resid 509 through 521 Processing helix chain '6' and resid 524 through 532 Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 592 Processing helix chain '6' and resid 626 through 631 removed outlier: 3.561A pdb=" N ALA 6 631 " --> pdb=" O ALA 6 627 " (cutoff:3.500A) Processing helix chain '6' and resid 645 through 650 Processing helix chain '6' and resid 651 through 658 removed outlier: 4.446A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU 6 657 " --> pdb=" O HIS 6 653 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 707 Processing helix chain '6' and resid 720 through 737 removed outlier: 3.743A pdb=" N THR 6 725 " --> pdb=" O GLU 6 721 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 760 removed outlier: 3.813A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR 6 754 " --> pdb=" O GLN 6 750 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 784 removed outlier: 3.592A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 814 removed outlier: 3.726A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 833 Processing helix chain '7' and resid 13 through 27 Processing helix chain '7' and resid 61 through 72 Processing helix chain '7' and resid 82 through 94 removed outlier: 3.636A pdb=" N LEU 7 94 " --> pdb=" O ASN 7 90 " (cutoff:3.500A) Processing helix chain '7' and resid 101 through 107 Processing helix chain '7' and resid 109 through 124 removed outlier: 4.094A pdb=" N PHE 7 113 " --> pdb=" O ASN 7 109 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 155 removed outlier: 4.008A pdb=" N MET 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) Processing helix chain '7' and resid 193 through 198 removed outlier: 3.853A pdb=" N THR 7 197 " --> pdb=" O PRO 7 193 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG 7 198 " --> pdb=" O PRO 7 194 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 193 through 198' Processing helix chain '7' and resid 212 through 216 Processing helix chain '7' and resid 226 through 230 Processing helix chain '7' and resid 231 through 235 removed outlier: 3.511A pdb=" N LEU 7 235 " --> pdb=" O GLY 7 232 " (cutoff:3.500A) Processing helix chain '7' and resid 286 through 293 Processing helix chain '7' and resid 363 through 369 Processing helix chain '7' and resid 396 through 408 Processing helix chain '7' and resid 409 through 419 removed outlier: 4.104A pdb=" N ALA 7 415 " --> pdb=" O TYR 7 411 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS 7 416 " --> pdb=" O ASN 7 412 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA 7 419 " --> pdb=" O ALA 7 415 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 530 through 544 Processing helix chain '7' and resid 579 through 584 removed outlier: 3.564A pdb=" N ILE 7 584 " --> pdb=" O PRO 7 580 " (cutoff:3.500A) Processing helix chain '7' and resid 587 through 593 removed outlier: 3.702A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 607 through 623 Processing helix chain '7' and resid 635 through 649 removed outlier: 4.077A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 675 Processing helix chain '7' and resid 685 through 703 Processing helix chain '7' and resid 709 through 727 removed outlier: 3.561A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 22 Processing helix chain 'A' and resid 33 through 61 Processing helix chain 'A' and resid 64 through 105 removed outlier: 3.511A pdb=" N ALA A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.799A pdb=" N ASN A 122 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.622A pdb=" N ASP A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 203 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.541A pdb=" N ASN B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 4.096A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'B' and resid 94 through 108 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 137 through 158 removed outlier: 3.793A pdb=" N GLY B 143 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 200 removed outlier: 3.535A pdb=" N ILE B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 3.839A pdb=" N GLU B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.346A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 117 through 140 removed outlier: 3.696A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU C 126 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 172 through 192 removed outlier: 3.528A pdb=" N LYS C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 13 Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.597A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 106 Processing helix chain 'D' and resid 123 through 154 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 170 through 174 Processing helix chain 'D' and resid 176 through 198 Processing helix chain 'D' and resid 199 through 202 Processing helix chain 'D' and resid 203 through 207 Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.814A pdb=" N LYS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 removed outlier: 4.886A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.597A pdb=" N ALA E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 52 Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 99 through 103 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 152 through 166 Processing helix chain 'E' and resid 224 through 241 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 284 through 303 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 333 through 341 Processing helix chain 'E' and resid 341 through 349 Processing helix chain 'E' and resid 352 through 367 removed outlier: 4.324A pdb=" N LYS E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 381 through 386 Processing helix chain 'E' and resid 387 through 395 Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 464 through 484 removed outlier: 3.624A pdb=" N PHE E 477 " --> pdb=" O TRP E 473 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 484 " --> pdb=" O SER E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 517 removed outlier: 3.698A pdb=" N ARG E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 540 removed outlier: 3.840A pdb=" N ARG E 540 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 558 removed outlier: 3.597A pdb=" N GLU E 558 " --> pdb=" O GLU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 599 removed outlier: 3.615A pdb=" N LYS E 599 " --> pdb=" O ILE E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 615 removed outlier: 3.626A pdb=" N ALA E 608 " --> pdb=" O ASN E 604 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 615 " --> pdb=" O GLN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 647 Processing helix chain 'F' and resid 672 through 680 removed outlier: 4.493A pdb=" N TYR F 676 " --> pdb=" O ALA F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 733 removed outlier: 3.793A pdb=" N GLY F 733 " --> pdb=" O TRP F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 787 Processing helix chain 'F' and resid 818 through 843 removed outlier: 3.996A pdb=" N GLU F 824 " --> pdb=" O SER F 820 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 840 " --> pdb=" O LEU F 836 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 842 " --> pdb=" O THR F 838 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 876 removed outlier: 3.513A pdb=" N ASP F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 887 removed outlier: 3.621A pdb=" N HIS F 887 " --> pdb=" O LEU F 883 " (cutoff:3.500A) Processing helix chain 'F' and resid 891 through 905 Processing helix chain 'F' and resid 907 through 923 removed outlier: 3.669A pdb=" N VAL F 911 " --> pdb=" O LEU F 907 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS F 912 " --> pdb=" O PRO F 908 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS F 913 " --> pdb=" O SER F 909 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU F 923 " --> pdb=" O GLU F 919 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 680 Processing helix chain 'G' and resid 724 through 733 removed outlier: 4.299A pdb=" N SER G 732 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY G 733 " --> pdb=" O TRP G 729 " (cutoff:3.500A) Processing helix chain 'G' and resid 782 through 787 Processing helix chain 'G' and resid 818 through 844 removed outlier: 3.837A pdb=" N ALA G 823 " --> pdb=" O VAL G 819 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU G 835 " --> pdb=" O LYS G 831 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR G 840 " --> pdb=" O LEU G 836 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU G 841 " --> pdb=" O LEU G 837 " (cutoff:3.500A) Processing helix chain 'G' and resid 850 through 876 Processing helix chain 'G' and resid 878 through 887 Processing helix chain 'G' and resid 891 through 903 Processing helix chain 'G' and resid 907 through 922 removed outlier: 3.905A pdb=" N VAL G 911 " --> pdb=" O LEU G 907 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS G 912 " --> pdb=" O PRO G 908 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS G 913 " --> pdb=" O SER G 909 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE G 914 " --> pdb=" O LEU G 910 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR G 922 " --> pdb=" O ARG G 918 " (cutoff:3.500A) Processing helix chain 'H' and resid 673 through 680 Processing helix chain 'H' and resid 724 through 733 removed outlier: 3.853A pdb=" N TRP H 729 " --> pdb=" O ASN H 725 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS H 730 " --> pdb=" O MET H 726 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET H 731 " --> pdb=" O GLU H 727 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER H 732 " --> pdb=" O ILE H 728 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY H 733 " --> pdb=" O TRP H 729 " (cutoff:3.500A) Processing helix chain 'H' and resid 818 through 843 removed outlier: 3.703A pdb=" N GLU H 824 " --> pdb=" O SER H 820 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU H 835 " --> pdb=" O LYS H 831 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU H 836 " --> pdb=" O VAL H 832 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR H 840 " --> pdb=" O LEU H 836 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU H 841 " --> pdb=" O LEU H 837 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU H 842 " --> pdb=" O THR H 838 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN H 843 " --> pdb=" O ASP H 839 " (cutoff:3.500A) Processing helix chain 'H' and resid 850 through 877 Processing helix chain 'H' and resid 878 through 886 Processing helix chain 'H' and resid 891 through 903 Processing helix chain 'H' and resid 907 through 923 removed outlier: 3.530A pdb=" N GLU H 923 " --> pdb=" O GLU H 919 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 32 removed outlier: 4.116A pdb=" N GLY K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 67 removed outlier: 3.525A pdb=" N ASP K 67 " --> pdb=" O LYS K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 81 Processing helix chain 'K' and resid 82 through 87 Processing helix chain 'K' and resid 87 through 106 removed outlier: 3.577A pdb=" N LEU K 92 " --> pdb=" O LEU K 88 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN K 97 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA K 106 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 137 removed outlier: 3.523A pdb=" N ILE K 124 " --> pdb=" O TYR K 120 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA K 125 " --> pdb=" O TYR K 121 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN K 127 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS K 128 " --> pdb=" O ILE K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 169 removed outlier: 3.545A pdb=" N ILE K 150 " --> pdb=" O SER K 146 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY K 154 " --> pdb=" O ILE K 150 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU K 155 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS K 158 " --> pdb=" O GLY K 154 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 173 Processing helix chain 'K' and resid 174 through 188 removed outlier: 3.621A pdb=" N ARG K 181 " --> pdb=" O ARG K 177 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA K 183 " --> pdb=" O ALA K 179 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL K 186 " --> pdb=" O LEU K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 214 removed outlier: 3.970A pdb=" N VAL K 201 " --> pdb=" O ARG K 197 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU K 202 " --> pdb=" O ASP K 198 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS K 203 " --> pdb=" O ASN K 199 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE K 208 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE K 209 " --> pdb=" O VAL K 205 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG K 210 " --> pdb=" O LEU K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 249 removed outlier: 3.635A pdb=" N SER K 249 " --> pdb=" O MET K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 260 Processing helix chain 'K' and resid 261 through 272 removed outlier: 3.834A pdb=" N PHE K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR K 270 " --> pdb=" O LEU K 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 290 removed outlier: 4.011A pdb=" N GLU K 288 " --> pdb=" O ILE K 284 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET K 290 " --> pdb=" O LEU K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 295 Processing helix chain 'K' and resid 299 through 303 Processing helix chain 'K' and resid 330 through 350 removed outlier: 4.332A pdb=" N GLU K 334 " --> pdb=" O SER K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 361 removed outlier: 3.841A pdb=" N GLY K 361 " --> pdb=" O SER K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 395 Processing helix chain 'K' and resid 417 through 421 removed outlier: 3.875A pdb=" N SER K 421 " --> pdb=" O LEU K 418 " (cutoff:3.500A) Processing helix chain 'K' and resid 430 through 461 removed outlier: 3.601A pdb=" N ILE K 441 " --> pdb=" O PHE K 437 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN K 442 " --> pdb=" O LYS K 438 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE K 449 " --> pdb=" O ILE K 445 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASN K 450 " --> pdb=" O ASP K 446 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE K 451 " --> pdb=" O SER K 447 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN K 458 " --> pdb=" O HIS K 454 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR K 459 " --> pdb=" O SER K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 493 removed outlier: 3.871A pdb=" N GLN K 472 " --> pdb=" O VAL K 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL K 473 " --> pdb=" O THR K 469 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU K 477 " --> pdb=" O VAL K 473 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE K 478 " --> pdb=" O GLU K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 503 removed outlier: 4.007A pdb=" N GLU K 503 " --> pdb=" O LYS K 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 506 through 523 removed outlier: 3.599A pdb=" N TYR K 521 " --> pdb=" O LEU K 517 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP K 522 " --> pdb=" O ARG K 518 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU K 523 " --> pdb=" O SER K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 549 removed outlier: 3.543A pdb=" N ILE K 534 " --> pdb=" O HIS K 530 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA K 535 " --> pdb=" O ALA K 531 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU K 538 " --> pdb=" O ILE K 534 " (cutoff:3.500A) Processing helix chain 'K' and resid 557 through 562 removed outlier: 4.091A pdb=" N VAL K 561 " --> pdb=" O ILE K 557 " (cutoff:3.500A) Processing helix chain 'K' and resid 567 through 580 removed outlier: 4.331A pdb=" N GLN K 571 " --> pdb=" O ASP K 567 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU K 572 " --> pdb=" O GLU K 568 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU K 576 " --> pdb=" O LEU K 572 " (cutoff:3.500A) Proline residue: K 577 - end of helix Processing helix chain 'K' and resid 581 through 583 No H-bonds generated for 'chain 'K' and resid 581 through 583' Processing helix chain 'K' and resid 584 through 602 removed outlier: 3.799A pdb=" N CYS K 591 " --> pdb=" O PHE K 587 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE K 592 " --> pdb=" O MET K 588 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU K 602 " --> pdb=" O VAL K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 603 through 605 No H-bonds generated for 'chain 'K' and resid 603 through 605' Processing helix chain 'K' and resid 658 through 663 Processing helix chain 'K' and resid 668 through 680 removed outlier: 3.814A pdb=" N PHE K 678 " --> pdb=" O THR K 674 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU K 679 " --> pdb=" O TYR K 675 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU K 680 " --> pdb=" O ILE K 676 " (cutoff:3.500A) Processing helix chain 'K' and resid 686 through 699 removed outlier: 3.545A pdb=" N VAL K 693 " --> pdb=" O SER K 689 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE K 697 " --> pdb=" O VAL K 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 711 removed outlier: 3.853A pdb=" N LEU K 709 " --> pdb=" O GLU K 706 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE K 711 " --> pdb=" O ALA K 708 " (cutoff:3.500A) Processing helix chain 'K' and resid 712 through 724 removed outlier: 3.726A pdb=" N ILE K 716 " --> pdb=" O ARG K 712 " (cutoff:3.500A) Processing helix chain 'K' and resid 734 through 755 removed outlier: 3.665A pdb=" N VAL K 738 " --> pdb=" O SER K 734 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS K 755 " --> pdb=" O LYS K 751 " (cutoff:3.500A) Processing helix chain 'K' and resid 758 through 763 Processing helix chain 'K' and resid 770 through 777 removed outlier: 3.764A pdb=" N PHE K 775 " --> pdb=" O SER K 771 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 61 Processing helix chain 'L' and resid 64 through 76 removed outlier: 5.201A pdb=" N HIS L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 103 removed outlier: 3.529A pdb=" N ASN L 87 " --> pdb=" O ASN L 83 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR L 95 " --> pdb=" O ILE L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 122 Processing helix chain 'L' and resid 122 through 138 removed outlier: 4.227A pdb=" N ARG L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY L 138 " --> pdb=" O ARG L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 1408 through 1412 Processing helix chain 'M' and resid 1436 through 1442 Processing helix chain 'M' and resid 1451 through 1462 removed outlier: 3.878A pdb=" N GLN M1460 " --> pdb=" O GLY M1456 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN M1461 " --> pdb=" O LYS M1457 " (cutoff:3.500A) Processing helix chain 'M' and resid 1525 through 1547 removed outlier: 4.328A pdb=" N MET M1535 " --> pdb=" O ILE M1531 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS M1538 " --> pdb=" O GLN M1534 " (cutoff:3.500A) Processing helix chain 'M' and resid 1565 through 1570 Processing helix chain 'M' and resid 1570 through 1584 Processing helix chain 'M' and resid 1597 through 1603 removed outlier: 3.986A pdb=" N THR M1603 " --> pdb=" O LYS M1599 " (cutoff:3.500A) Processing helix chain 'M' and resid 1603 through 1608 Processing helix chain 'M' and resid 1629 through 1642 removed outlier: 3.868A pdb=" N LYS M1633 " --> pdb=" O PRO M1629 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS M1634 " --> pdb=" O THR M1630 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU M1635 " --> pdb=" O LEU M1631 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL M1636 " --> pdb=" O LEU M1632 " (cutoff:3.500A) Processing helix chain 'M' and resid 1644 through 1656 removed outlier: 3.901A pdb=" N HIS M1648 " --> pdb=" O SER M1644 " (cutoff:3.500A) Processing helix chain 'M' and resid 1666 through 1683 removed outlier: 3.816A pdb=" N TYR M1670 " --> pdb=" O ASP M1666 " (cutoff:3.500A) Processing helix chain 'M' and resid 1700 through 1704 removed outlier: 3.903A pdb=" N ASP M1704 " --> pdb=" O ILE M1701 " (cutoff:3.500A) Processing helix chain 'M' and resid 1706 through 1714 Processing helix chain 'M' and resid 1738 through 1747 Processing helix chain 'M' and resid 1784 through 1804 Processing helix chain 'M' and resid 1806 through 1820 removed outlier: 3.608A pdb=" N ASP M1810 " --> pdb=" O ASN M1806 " (cutoff:3.500A) Processing helix chain 'M' and resid 1829 through 1855 Processing helix chain 'M' and resid 1878 through 1892 removed outlier: 3.764A pdb=" N ASN M1892 " --> pdb=" O ALA M1888 " (cutoff:3.500A) Processing helix chain 'M' and resid 1893 through 1896 Processing helix chain 'M' and resid 1941 through 1945 Processing helix chain 'M' and resid 1948 through 1976 removed outlier: 4.322A pdb=" N GLU M1952 " --> pdb=" O ILE M1948 " (cutoff:3.500A) Processing helix chain 'M' and resid 2002 through 2026 removed outlier: 3.925A pdb=" N LEU M2006 " --> pdb=" O GLY M2002 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE M2007 " --> pdb=" O PHE M2003 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LYS M2009 " --> pdb=" O HIS M2005 " (cutoff:3.500A) Proline residue: M2010 - end of helix Processing helix chain 'M' and resid 2049 through 2064 Processing helix chain 'M' and resid 2068 through 2083 removed outlier: 3.714A pdb=" N ILE M2082 " --> pdb=" O GLU M2078 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE M2083 " --> pdb=" O LEU M2079 " (cutoff:3.500A) Processing helix chain 'M' and resid 2123 through 2127 Processing helix chain 'M' and resid 2138 through 2159 Processing helix chain 'M' and resid 2190 through 2209 removed outlier: 3.623A pdb=" N ILE M2194 " --> pdb=" O PRO M2190 " (cutoff:3.500A) Processing helix chain 'M' and resid 2210 through 2221 removed outlier: 3.683A pdb=" N THR M2221 " --> pdb=" O ILE M2217 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 26 removed outlier: 3.636A pdb=" N LEU N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Proline residue: N 19 - end of helix Processing helix chain 'N' and resid 34 through 49 Processing helix chain 'N' and resid 55 through 70 Processing helix chain 'N' and resid 79 through 96 Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 210 through 237 removed outlier: 3.521A pdb=" N LYS N 214 " --> pdb=" O ASP N 210 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE N 218 " --> pdb=" O LYS N 214 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU N 219 " --> pdb=" O VAL N 215 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG N 221 " --> pdb=" O MET N 217 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN N 234 " --> pdb=" O MET N 230 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE N 235 " --> pdb=" O ARG N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 275 removed outlier: 4.015A pdb=" N LEU N 275 " --> pdb=" O LYS N 272 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 360 removed outlier: 3.601A pdb=" N THR N 358 " --> pdb=" O ILE N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 381 through 394 Processing helix chain 'N' and resid 410 through 427 removed outlier: 3.724A pdb=" N ASP N 426 " --> pdb=" O GLN N 422 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP N 427 " --> pdb=" O LYS N 423 " (cutoff:3.500A) Processing helix chain 'N' and resid 453 through 471 removed outlier: 3.521A pdb=" N PHE N 458 " --> pdb=" O SER N 454 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG N 471 " --> pdb=" O THR N 467 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 497 removed outlier: 3.844A pdb=" N SER N 496 " --> pdb=" O GLY N 492 " (cutoff:3.500A) Processing helix chain 'N' and resid 509 through 512 Processing helix chain 'N' and resid 513 through 520 Processing helix chain 'N' and resid 545 through 554 Processing helix chain 'N' and resid 595 through 610 Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 245 removed outlier: 6.287A pdb=" N LEU 2 242 " --> pdb=" O ARG 2 296 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER 2 298 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL 2 244 " --> pdb=" O SER 2 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 317 through 318 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 317 through 318 current: chain '2' and resid 382 through 391 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 405 through 410 current: chain '2' and resid 448 through 458 Processing sheet with id=AA3, first strand: chain '2' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain '2' and resid 339 through 341 removed outlier: 4.274A pdb=" N ARG 2 374 " --> pdb=" O ASN 2 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 526 through 527 Processing sheet with id=AA6, first strand: chain '2' and resid 563 through 567 removed outlier: 6.308A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA 2 566 " --> pdb=" O ASP 2 607 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL 2 539 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA 2 650 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU 2 542 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '2' and resid 578 through 582 Processing sheet with id=AA8, first strand: chain '2' and resid 630 through 633 Processing sheet with id=AA9, first strand: chain '3' and resid 95 through 99 Processing sheet with id=AB1, first strand: chain '3' and resid 165 through 166 removed outlier: 6.463A pdb=" N ASN 3 293 " --> pdb=" O VAL 3 326 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL 3 326 " --> pdb=" O ASN 3 293 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL 3 295 " --> pdb=" O ASN 3 324 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N SER 3 273 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N ILE 3 321 " --> pdb=" O SER 3 273 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP 3 275 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY 3 323 " --> pdb=" O ASP 3 275 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR 3 257 " --> pdb=" O THR 3 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 195 through 202 Processing sheet with id=AB3, first strand: chain '3' and resid 429 through 433 removed outlier: 6.762A pdb=" N ILE 3 430 " --> pdb=" O CYS 3 471 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP 3 473 " --> pdb=" O ILE 3 430 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 444 through 448 Processing sheet with id=AB5, first strand: chain '3' and resid 494 through 497 Processing sheet with id=AB6, first strand: chain '4' and resid 324 through 335 removed outlier: 7.113A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N SER 4 414 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N VAL 4 461 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER 4 416 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL 4 463 " --> pdb=" O SER 4 416 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS 4 418 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N HIS 4 465 " --> pdb=" O CYS 4 418 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS 4 324 " --> pdb=" O PHE 4 439 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 339 through 344 removed outlier: 6.750A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 355 through 356 Processing sheet with id=AB9, first strand: chain '4' and resid 444 through 445 removed outlier: 4.455A pdb=" N ILE 4 444 " --> pdb=" O LYS 4 454 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 591 through 592 removed outlier: 3.661A pdb=" N LEU 4 672 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 604 through 607 removed outlier: 3.714A pdb=" N GLU 4 617 " --> pdb=" O TYR 4 604 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC4, first strand: chain '4' and resid 761 through 762 removed outlier: 6.859A pdb=" N ILE 4 761 " --> pdb=" O VAL 4 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '4' and resid 916 through 918 Processing sheet with id=AC6, first strand: chain '5' and resid 60 through 64 Processing sheet with id=AC7, first strand: chain '5' and resid 159 through 169 removed outlier: 6.764A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE 5 330 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 173 through 183 Processing sheet with id=AC9, first strand: chain '5' and resid 398 through 399 Processing sheet with id=AD1, first strand: chain '5' and resid 436 through 440 removed outlier: 6.572A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '5' and resid 451 through 455 Processing sheet with id=AD3, first strand: chain '5' and resid 501 through 506 Processing sheet with id=AD4, first strand: chain '5' and resid 613 through 614 removed outlier: 6.863A pdb=" N ARG 5 613 " --> pdb=" O ALA 5 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain '5' and resid 727 through 729 Processing sheet with id=AD6, first strand: chain '6' and resid 150 through 154 removed outlier: 3.548A pdb=" N ILE 6 151 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 287 through 288 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 287 through 288 current: chain '6' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 317 through 322 current: chain '6' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 376 through 382 current: chain '6' and resid 450 through 461 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '6' and resid 596 through 599 removed outlier: 6.482A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS 6 572 " --> pdb=" O PHE 6 713 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE 6 715 " --> pdb=" O CYS 6 572 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL 6 574 " --> pdb=" O ILE 6 715 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 610 through 614 Processing sheet with id=AE1, first strand: chain '6' and resid 660 through 664 Processing sheet with id=AE2, first strand: chain '6' and resid 764 through 765 removed outlier: 6.778A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain '7' and resid 77 through 81 removed outlier: 6.283A pdb=" N VAL 7 78 " --> pdb=" O TYR 7 203 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS 7 205 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE 7 80 " --> pdb=" O LYS 7 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain '7' and resid 238 through 244 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 244 current: chain '7' and resid 268 through 272 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 268 through 272 current: chain '7' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 330 through 336 current: chain '7' and resid 373 through 383 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain '7' and resid 481 through 484 removed outlier: 7.107A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL 7 456 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '7' and resid 545 through 547 Processing sheet with id=AE7, first strand: chain 'A' and resid 162 through 166 removed outlier: 3.646A pdb=" N SER E 56 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU E 81 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU E 123 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU E 83 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE E 120 " --> pdb=" O GLN E 141 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.878A pdb=" N GLY A 172 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 24 through 27 Processing sheet with id=AF1, first strand: chain 'C' and resid 43 through 47 Processing sheet with id=AF2, first strand: chain 'D' and resid 274 through 278 Processing sheet with id=AF3, first strand: chain 'D' and resid 255 through 260 Processing sheet with id=AF4, first strand: chain 'E' and resid 316 through 322 Processing sheet with id=AF5, first strand: chain 'E' and resid 526 through 530 removed outlier: 3.521A pdb=" N LEU E 569 " --> pdb=" O ALA E 582 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER E 571 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 492 through 496 removed outlier: 6.676A pdb=" N VAL F 502 " --> pdb=" O LEU F 494 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET F 496 " --> pdb=" O GLY F 500 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY F 500 " --> pdb=" O MET F 496 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 505 " --> pdb=" O SER F 512 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 536 through 539 Processing sheet with id=AF8, first strand: chain 'F' and resid 581 through 583 removed outlier: 3.741A pdb=" N ALA F 608 " --> pdb=" O SER F 599 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 615 through 620 removed outlier: 3.804A pdb=" N ALA F 617 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 628 " --> pdb=" O ALA F 617 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 703 through 707 removed outlier: 6.522A pdb=" N LEU F 704 " --> pdb=" O ILE F 721 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 740 through 748 removed outlier: 6.756A pdb=" N ASN F 753 " --> pdb=" O LEU F 745 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU F 747 " --> pdb=" O THR F 751 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR F 751 " --> pdb=" O LEU F 747 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.784A pdb=" N VAL G 502 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL G 515 " --> pdb=" O TYR G 526 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 536 through 539 removed outlier: 3.521A pdb=" N GLY G 547 " --> pdb=" O LEU G 536 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 553 through 554 Processing sheet with id=AG6, first strand: chain 'G' and resid 581 through 583 Processing sheet with id=AG7, first strand: chain 'G' and resid 615 through 620 removed outlier: 3.721A pdb=" N ALA G 617 " --> pdb=" O VAL G 628 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR G 638 " --> pdb=" O GLU G 654 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU G 654 " --> pdb=" O TYR G 638 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS G 652 " --> pdb=" O LEU G 640 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU G 642 " --> pdb=" O TYR G 650 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR G 650 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 684 through 686 removed outlier: 4.471A pdb=" N GLY G 699 " --> pdb=" O THR G 703 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR G 703 " --> pdb=" O GLY G 699 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU G 722 " --> pdb=" O LEU G 704 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 742 through 744 Processing sheet with id=AH1, first strand: chain 'H' and resid 492 through 496 removed outlier: 5.834A pdb=" N TYR H 493 " --> pdb=" O THR H 504 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR H 504 " --> pdb=" O TYR H 493 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR H 495 " --> pdb=" O VAL H 502 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR H 511 " --> pdb=" O ASP H 530 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE H 513 " --> pdb=" O PHE H 528 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE H 528 " --> pdb=" O ILE H 513 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL H 515 " --> pdb=" O TYR H 526 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 536 through 540 removed outlier: 3.601A pdb=" N GLY H 543 " --> pdb=" O ASN H 540 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 578 through 583 removed outlier: 4.115A pdb=" N SER H 580 " --> pdb=" O GLY H 591 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER H 599 " --> pdb=" O PHE H 607 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 615 through 620 removed outlier: 3.559A pdb=" N ALA H 617 " --> pdb=" O VAL H 628 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR H 619 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR H 638 " --> pdb=" O ARG H 653 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG H 653 " --> pdb=" O TYR H 638 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU H 640 " --> pdb=" O TYR H 651 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR H 651 " --> pdb=" O LEU H 640 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 703 through 706 removed outlier: 6.222A pdb=" N LEU H 704 " --> pdb=" O ILE H 721 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 742 through 747 removed outlier: 6.800A pdb=" N ASN H 753 " --> pdb=" O LEU H 745 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 363 through 368 removed outlier: 3.510A pdb=" N LEU K 364 " --> pdb=" O VAL K 376 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU K 374 " --> pdb=" O ILE K 366 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR K 368 " --> pdb=" O THR K 372 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 1320 through 1321 removed outlier: 3.625A pdb=" N PHE M1447 " --> pdb=" O MET M1470 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET M1470 " --> pdb=" O PHE M1447 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 1337 through 1341 removed outlier: 3.590A pdb=" N VAL M1340 " --> pdb=" O GLN M1347 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N PHE M1463 " --> pdb=" O ASN M1348 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR M1350 " --> pdb=" O PHE M1463 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 1487 through 1488 removed outlier: 3.830A pdb=" N GLN M1593 " --> pdb=" O LEU M1487 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU M1590 " --> pdb=" O VAL M1613 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 1508 through 1511 removed outlier: 3.554A pdb=" N ILE M1509 " --> pdb=" O ASN M1557 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 1721 through 1722 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 1721 through 1722 current: chain 'M' and resid 1866 through 1870 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 1866 through 1870 current: chain 'M' and resid 1916 through 1921 Processing sheet with id=AI4, first strand: chain 'M' and resid 2102 through 2107 removed outlier: 3.763A pdb=" N ASP M2105 " --> pdb=" O SER M2115 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER M2115 " --> pdb=" O ASP M2105 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 2162 through 2164 Processing sheet with id=AI6, first strand: chain 'N' and resid 172 through 173 removed outlier: 6.892A pdb=" N VAL N 540 " --> pdb=" O VAL N 640 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS N 642 " --> pdb=" O VAL N 540 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE N 542 " --> pdb=" O CYS N 642 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 183 through 184 Processing sheet with id=AI8, first strand: chain 'N' and resid 281 through 290 removed outlier: 5.071A pdb=" N TRP N 296 " --> pdb=" O ILE N 307 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N PHE N 339 " --> pdb=" O SER N 304 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU N 306 " --> pdb=" O PHE N 339 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL N 341 " --> pdb=" O GLU N 306 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP N 308 " --> pdb=" O VAL N 341 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SER N 343 " --> pdb=" O ASP N 308 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU N 329 " --> pdb=" O THR N 342 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET N 344 " --> pdb=" O LEU N 327 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU N 327 " --> pdb=" O MET N 344 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 523 through 525 2987 hydrogen bonds defined for protein. 8547 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: 34.75 Time building geometry restraints manager: 15.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 22995 1.35 - 1.50: 18980 1.50 - 1.65: 29549 1.65 - 1.80: 295 1.80 - 1.95: 208 Bond restraints: 72027 Sorted by residual: bond pdb=" N CYS 4 567 " pdb=" CA CYS 4 567 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.58e+01 bond pdb=" C ASP M1810 " pdb=" O ASP M1810 " ideal model delta sigma weight residual 1.237 1.289 -0.052 1.17e-02 7.31e+03 1.98e+01 bond pdb=" C ASN M1814 " pdb=" O ASN M1814 " ideal model delta sigma weight residual 1.237 1.286 -0.049 1.17e-02 7.31e+03 1.78e+01 bond pdb=" N LEU K 414 " pdb=" CA LEU K 414 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.71e+01 bond pdb=" C GLN A 18 " pdb=" O GLN A 18 " ideal model delta sigma weight residual 1.237 1.280 -0.043 1.17e-02 7.31e+03 1.35e+01 ... (remaining 72022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 95795 1.91 - 3.81: 1656 3.81 - 5.72: 182 5.72 - 7.63: 25 7.63 - 9.54: 14 Bond angle restraints: 97672 Sorted by residual: angle pdb=" N LEU B 160 " pdb=" CA LEU B 160 " pdb=" C LEU B 160 " ideal model delta sigma weight residual 113.19 104.38 8.81 1.19e+00 7.06e-01 5.48e+01 angle pdb=" N LYS 7 364 " pdb=" CA LYS 7 364 " pdb=" C LYS 7 364 " ideal model delta sigma weight residual 112.87 105.17 7.70 1.20e+00 6.94e-01 4.12e+01 angle pdb=" C ASP M1810 " pdb=" N LEU M1811 " pdb=" CA LEU M1811 " ideal model delta sigma weight residual 120.54 112.86 7.68 1.35e+00 5.49e-01 3.24e+01 angle pdb=" C CYS 4 567 " pdb=" CA CYS 4 567 " pdb=" CB CYS 4 567 " ideal model delta sigma weight residual 117.07 109.28 7.79 1.44e+00 4.82e-01 2.93e+01 angle pdb=" C TYR 2 194 " pdb=" N SER 2 195 " pdb=" CA SER 2 195 " ideal model delta sigma weight residual 120.38 113.56 6.82 1.37e+00 5.33e-01 2.48e+01 ... (remaining 97667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.73: 42346 33.73 - 67.46: 1345 67.46 - 101.19: 89 101.19 - 134.92: 2 134.92 - 168.65: 4 Dihedral angle restraints: 43786 sinusoidal: 18253 harmonic: 25533 Sorted by residual: dihedral pdb=" C5' ADP 31001 " pdb=" O5' ADP 31001 " pdb=" PA ADP 31001 " pdb=" O2A ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 108.65 -168.65 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PA ADP 31001 " pdb=" PB ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 97.90 -157.90 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" O1B ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PB ADP 31001 " pdb=" PA ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 74.94 -134.95 1 2.00e+01 2.50e-03 4.10e+01 ... (remaining 43783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 8594 0.047 - 0.094: 1960 0.094 - 0.140: 524 0.140 - 0.187: 60 0.187 - 0.234: 18 Chirality restraints: 11156 Sorted by residual: chirality pdb=" CA VAL 4 771 " pdb=" N VAL 4 771 " pdb=" C VAL 4 771 " pdb=" CB VAL 4 771 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE 5 333 " pdb=" N ILE 5 333 " pdb=" C ILE 5 333 " pdb=" CB ILE 5 333 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU M1816 " pdb=" N LEU M1816 " pdb=" C LEU M1816 " pdb=" CB LEU M1816 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 11153 not shown) Planarity restraints: 12268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 4 790 " -0.748 9.50e-02 1.11e+02 3.36e-01 6.85e+01 pdb=" NE ARG 4 790 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG 4 790 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG 4 790 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 4 790 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 159 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C GLY B 159 " 0.074 2.00e-02 2.50e+03 pdb=" O GLY B 159 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 160 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER 3 300 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C SER 3 300 " -0.066 2.00e-02 2.50e+03 pdb=" O SER 3 300 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU 3 301 " 0.022 2.00e-02 2.50e+03 ... (remaining 12265 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 597 2.54 - 3.13: 56192 3.13 - 3.72: 112487 3.72 - 4.31: 153592 4.31 - 4.90: 257959 Nonbonded interactions: 580827 Sorted by model distance: nonbonded pdb=" O3G AGS 5 802 " pdb="MG MG 5 803 " model vdw 1.954 2.170 nonbonded pdb=" OG SER 5 423 " pdb="MG MG 5 803 " model vdw 1.973 2.170 nonbonded pdb=" O2B ADP 31001 " pdb="MG MG 31002 " model vdw 2.017 2.170 nonbonded pdb="MG MG 61102 " pdb=" O1B AGS 61103 " model vdw 2.044 2.170 nonbonded pdb=" OG SER 6 582 " pdb="MG MG 61102 " model vdw 2.048 2.170 ... (remaining 580822 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 'F' and (resid 474 through 490 or (resid 491 and (name N or name CA or na \ me C or name O or name CB )) or resid 492 through 576 or (resid 577 and (name N \ or name CA or name C or name O or name CB )) or resid 578 through 586 or (resid \ 587 and (name N or name CA or name C or name O or name CB )) or resid 588 throug \ h 665 or resid 670 through 782 or (resid 783 and (name N or name CA or name C or \ name O or name CB )) or resid 784 or resid 816 through 889 or (resid 890 and (n \ ame N or name CA or name C or name O or name CB )) or resid 891 through 899 or ( \ resid 900 and (name N or name CA or name C or name O or name CB )) or resid 901 \ or (resid 902 and (name N or name CA or name C or name O or name CB )) or resid \ 903 through 922)) selection = (chain 'G' and (resid 474 through 490 or (resid 491 and (name N or name CA or na \ me C or name O or name CB )) or resid 492 through 586 or (resid 587 and (name N \ or name CA or name C or name O or name CB )) or resid 588 through 665 or resid 6 \ 70 through 782 or (resid 783 and (name N or name CA or name C or name O or name \ CB )) or resid 784 or resid 816 through 901 or (resid 902 and (name N or name CA \ or name C or name O or name CB )) or resid 903 through 909 or (resid 910 and (n \ ame N or name CA or name C or name O or name CB )) or resid 911 through 922)) selection = (chain 'H' and (resid 474 through 576 or (resid 577 and (name N or name CA or na \ me C or name O or name CB )) or resid 578 through 784 or resid 816 through 889 o \ r (resid 890 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 91 through 899 or (resid 900 and (name N or name CA or name C or name O or name \ CB )) or resid 901 through 909 or (resid 910 and (name N or name CA or name C or \ name O or name CB )) or resid 911 through 922)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.800 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: 0.050 Extract box with map and model: 2.010 Check model and map are aligned: 0.410 Set scattering table: 0.490 Process input model: 143.820 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.004 0.052 72027 Z= 0.278 Angle : 0.587 9.537 97672 Z= 0.348 Chirality : 0.044 0.234 11156 Planarity : 0.005 0.336 12268 Dihedral : 15.738 168.649 27190 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.09 % Favored : 94.75 % Rotamer: Outliers : 1.30 % Allowed : 0.80 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 8553 helix: 1.19 (0.09), residues: 3614 sheet: -1.00 (0.15), residues: 1274 loop : -0.78 (0.11), residues: 3665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP E 473 HIS 0.004 0.001 HIS 6 669 PHE 0.029 0.001 PHE 7 355 TYR 0.021 0.001 TYR E 2 ARG 0.016 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 339 time to evaluate : 6.344 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: 2 501 MET cc_start: 0.8957 (mmt) cc_final: 0.8498 (mmt) REVERT: 3 280 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: 4 777 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7906 (mtp) REVERT: 4 792 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8025 (p) REVERT: 4 874 LYS cc_start: 0.4528 (OUTLIER) cc_final: 0.3534 (mmtt) REVERT: 7 402 MET cc_start: 0.8263 (tpt) cc_final: 0.8052 (tpp) REVERT: 7 541 MET cc_start: 0.8078 (ttt) cc_final: 0.7874 (ttp) REVERT: A 20 TYR cc_start: 0.7564 (t80) cc_final: 0.7327 (t80) REVERT: A 100 MET cc_start: 0.8387 (mtp) cc_final: 0.8046 (mtp) REVERT: B 63 MET cc_start: 0.9278 (mtm) cc_final: 0.8857 (mtp) REVERT: F 778 MET cc_start: 0.4680 (mmt) cc_final: 0.4028 (mmm) REVERT: G 726 MET cc_start: 0.3043 (ttt) cc_final: 0.2750 (ttp) REVERT: H 477 MET cc_start: 0.6543 (mpp) cc_final: 0.6313 (mpp) REVERT: M 1805 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: M 2107 LEU cc_start: 0.9019 (tt) cc_final: 0.8668 (tp) REVERT: N 91 MET cc_start: 0.6836 (ppp) cc_final: 0.6599 (ppp) outliers start: 100 outliers final: 37 residues processed: 430 average time/residue: 0.6461 time to fit residues: 481.7530 Evaluate side-chains 331 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 289 time to evaluate : 6.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 3 residue 280 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 313 THR Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 4 residue 574 LYS Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 772 ARG Chi-restraints excluded: chain 4 residue 777 MET Chi-restraints excluded: chain 4 residue 782 ASP Chi-restraints excluded: chain 4 residue 792 THR Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 4 residue 869 ILE Chi-restraints excluded: chain 4 residue 874 LYS Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 341 SER Chi-restraints excluded: chain 6 residue 737 LYS Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 555 GLN Chi-restraints excluded: chain H residue 557 ARG Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 631 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain M residue 1411 LYS Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1583 GLU Chi-restraints excluded: chain M residue 1797 GLU Chi-restraints excluded: chain M residue 1800 ASP Chi-restraints excluded: chain M residue 1805 GLU Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1812 LEU Chi-restraints excluded: chain M residue 1815 SER Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1819 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 732 optimal weight: 7.9990 chunk 657 optimal weight: 10.0000 chunk 365 optimal weight: 6.9990 chunk 224 optimal weight: 0.4980 chunk 443 optimal weight: 0.8980 chunk 351 optimal weight: 0.8980 chunk 680 optimal weight: 20.0000 chunk 263 optimal weight: 9.9990 chunk 413 optimal weight: 0.9980 chunk 506 optimal weight: 3.9990 chunk 788 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 200 GLN 3 164 HIS 3 310 ASN 3 312 ASN 3 507 ASN 4 377 ASN ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 198 ASN ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 210 ASN 7 683 GLN A 24 ASN A 71 GLN C 136 ASN E 296 GLN E 550 ASN E 624 ASN F 843 ASN H 680 ASN M1385 ASN ** M1806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN ** M2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 72027 Z= 0.215 Angle : 0.526 13.492 97672 Z= 0.275 Chirality : 0.041 0.211 11156 Planarity : 0.004 0.060 12268 Dihedral : 10.518 163.279 10211 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.67 % Allowed : 5.92 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 8553 helix: 1.33 (0.09), residues: 3675 sheet: -1.04 (0.15), residues: 1306 loop : -0.71 (0.11), residues: 3572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP G 718 HIS 0.006 0.001 HIS 2 868 PHE 0.019 0.001 PHE 7 355 TYR 0.025 0.001 TYR F 862 ARG 0.007 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 310 time to evaluate : 6.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 501 MET cc_start: 0.8929 (mmt) cc_final: 0.8620 (mmt) REVERT: 4 777 MET cc_start: 0.8615 (mtm) cc_final: 0.8336 (mtp) REVERT: A 100 MET cc_start: 0.8392 (mtp) cc_final: 0.8063 (mtp) REVERT: B 63 MET cc_start: 0.9276 (mtm) cc_final: 0.9019 (mtp) REVERT: F 726 MET cc_start: 0.8621 (tpp) cc_final: 0.8404 (tpt) REVERT: F 778 MET cc_start: 0.4448 (mmt) cc_final: 0.3892 (mmm) REVERT: H 477 MET cc_start: 0.6292 (mpp) cc_final: 0.5848 (mpp) REVERT: M 2107 LEU cc_start: 0.9093 (tt) cc_final: 0.8810 (tp) outliers start: 52 outliers final: 30 residues processed: 351 average time/residue: 0.6508 time to fit residues: 403.8730 Evaluate side-chains 309 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 279 time to evaluate : 6.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 802 ILE Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 4 residue 869 ILE Chi-restraints excluded: chain 5 residue 21 ASP Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1805 GLU Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1812 LEU Chi-restraints excluded: chain M residue 1889 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 438 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 656 optimal weight: 4.9990 chunk 536 optimal weight: 10.0000 chunk 217 optimal weight: 0.0870 chunk 789 optimal weight: 0.4980 chunk 853 optimal weight: 2.9990 chunk 703 optimal weight: 5.9990 chunk 783 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 633 optimal weight: 10.0000 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 646 HIS 5 198 ASN ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS E 402 GLN F 843 ASN F 916 ASN M1534 GLN M1806 ASN M1821 GLN M1838 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 72027 Z= 0.237 Angle : 0.507 8.782 97672 Z= 0.264 Chirality : 0.041 0.192 11156 Planarity : 0.004 0.069 12268 Dihedral : 10.183 165.267 10154 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.73 % Allowed : 8.89 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.10), residues: 8553 helix: 1.44 (0.09), residues: 3669 sheet: -1.10 (0.15), residues: 1311 loop : -0.70 (0.11), residues: 3573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 473 HIS 0.013 0.001 HIS G 563 PHE 0.021 0.001 PHE 2 271 TYR 0.023 0.001 TYR 5 730 ARG 0.010 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 293 time to evaluate : 6.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 501 MET cc_start: 0.8897 (mmt) cc_final: 0.8572 (mmt) REVERT: 2 743 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7652 (ttm110) REVERT: 4 777 MET cc_start: 0.8567 (mtm) cc_final: 0.8345 (mtp) REVERT: 4 881 MET cc_start: 0.7895 (pmm) cc_final: 0.7471 (pmm) REVERT: 6 726 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: 7 506 MET cc_start: 0.5519 (ppp) cc_final: 0.5075 (ppp) REVERT: 7 600 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8384 (ptp) REVERT: A 100 MET cc_start: 0.8403 (mtp) cc_final: 0.8201 (mtp) REVERT: B 63 MET cc_start: 0.9307 (mtm) cc_final: 0.8934 (mtp) REVERT: C 36 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7309 (tpt170) REVERT: F 726 MET cc_start: 0.8650 (tpp) cc_final: 0.8326 (tpt) REVERT: F 778 MET cc_start: 0.4164 (mmt) cc_final: 0.3793 (mmm) REVERT: H 477 MET cc_start: 0.6161 (mpp) cc_final: 0.5669 (mpp) REVERT: K 675 TYR cc_start: 0.4218 (OUTLIER) cc_final: 0.3806 (t80) REVERT: M 2107 LEU cc_start: 0.9141 (tt) cc_final: 0.8858 (tp) outliers start: 56 outliers final: 33 residues processed: 338 average time/residue: 0.6833 time to fit residues: 413.2170 Evaluate side-chains 316 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 279 time to evaluate : 6.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 21 ASP Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1812 LEU Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1889 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 780 optimal weight: 6.9990 chunk 593 optimal weight: 7.9990 chunk 409 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 376 optimal weight: 6.9990 chunk 530 optimal weight: 7.9990 chunk 792 optimal weight: 8.9990 chunk 839 optimal weight: 5.9990 chunk 414 optimal weight: 1.9990 chunk 751 optimal weight: 9.9990 chunk 226 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 652 GLN ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS E 296 GLN E 624 ASN M1838 ASN ** M2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 72027 Z= 0.316 Angle : 0.525 9.227 97672 Z= 0.272 Chirality : 0.041 0.204 11156 Planarity : 0.004 0.062 12268 Dihedral : 10.135 175.389 10142 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.04 % Allowed : 10.28 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.10), residues: 8553 helix: 1.41 (0.09), residues: 3673 sheet: -1.17 (0.15), residues: 1330 loop : -0.71 (0.11), residues: 3550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 473 HIS 0.011 0.001 HIS 7 622 PHE 0.026 0.001 PHE 2 271 TYR 0.021 0.001 TYR 5 46 ARG 0.010 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 285 time to evaluate : 6.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 743 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7670 (ttm170) REVERT: 4 881 MET cc_start: 0.7962 (pmm) cc_final: 0.7566 (pmm) REVERT: 6 726 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: 7 506 MET cc_start: 0.5534 (ppp) cc_final: 0.5163 (ppp) REVERT: 7 600 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8300 (ptp) REVERT: B 63 MET cc_start: 0.9378 (mtm) cc_final: 0.8966 (mtp) REVERT: C 5 ASP cc_start: 0.8604 (t0) cc_final: 0.8212 (t0) REVERT: F 726 MET cc_start: 0.8613 (tpp) cc_final: 0.8370 (tpt) REVERT: F 778 MET cc_start: 0.4124 (mmt) cc_final: 0.3795 (mmm) REVERT: H 707 LEU cc_start: 0.3218 (OUTLIER) cc_final: 0.2940 (mp) REVERT: H 835 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: K 675 TYR cc_start: 0.4250 (OUTLIER) cc_final: 0.3811 (t80) REVERT: M 2107 LEU cc_start: 0.9161 (tt) cc_final: 0.8897 (tp) outliers start: 80 outliers final: 53 residues processed: 353 average time/residue: 0.6953 time to fit residues: 441.3274 Evaluate side-chains 335 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 277 time to evaluate : 6.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 2 residue 323 VAL Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 21 ASP Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 341 SER Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 707 LEU Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 566 SER Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1838 ASN Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 698 optimal weight: 4.9990 chunk 476 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 624 optimal weight: 20.0000 chunk 346 optimal weight: 4.9990 chunk 715 optimal weight: 20.0000 chunk 579 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 428 optimal weight: 0.5980 chunk 753 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 531 GLN 5 58 ASN ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN E 624 ASN ** M2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 72027 Z= 0.392 Angle : 0.551 8.878 97672 Z= 0.284 Chirality : 0.042 0.226 11156 Planarity : 0.004 0.062 12268 Dihedral : 10.104 148.463 10140 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.18 % Allowed : 11.63 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.09), residues: 8553 helix: 1.35 (0.09), residues: 3669 sheet: -1.24 (0.15), residues: 1315 loop : -0.76 (0.11), residues: 3569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 473 HIS 0.005 0.001 HIS M1837 PHE 0.027 0.001 PHE 2 271 TYR 0.024 0.001 TYR 5 730 ARG 0.010 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 280 time to evaluate : 7.813 Fit side-chains revert: symmetry clash REVERT: 4 881 MET cc_start: 0.8000 (pmm) cc_final: 0.7593 (pmm) REVERT: 6 726 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: 7 506 MET cc_start: 0.5803 (ppp) cc_final: 0.5445 (ppp) REVERT: 7 600 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8293 (ptp) REVERT: A 14 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8822 (ttmm) REVERT: B 63 MET cc_start: 0.9379 (mtm) cc_final: 0.8990 (mtp) REVERT: F 726 MET cc_start: 0.8620 (tpp) cc_final: 0.8348 (tpt) REVERT: F 778 MET cc_start: 0.4087 (mmt) cc_final: 0.3776 (mmm) REVERT: H 477 MET cc_start: 0.6020 (mpp) cc_final: 0.5269 (mpp) REVERT: H 707 LEU cc_start: 0.3199 (OUTLIER) cc_final: 0.2905 (mp) REVERT: H 835 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: K 675 TYR cc_start: 0.4323 (OUTLIER) cc_final: 0.3874 (t80) REVERT: M 1668 MET cc_start: 0.6632 (mpp) cc_final: 0.6328 (mmm) outliers start: 91 outliers final: 68 residues processed: 358 average time/residue: 0.6233 time to fit residues: 402.0363 Evaluate side-chains 349 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 275 time to evaluate : 6.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 343 THR Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 323 ASP Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 438 THR Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 21 ASP Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 341 SER Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 668 ILE Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 707 LEU Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain H residue 757 VAL Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 566 SER Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1416 SER Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 282 optimal weight: 0.8980 chunk 755 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 492 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 839 optimal weight: 4.9990 chunk 697 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 277 optimal weight: 0.8980 chunk 440 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 GLN 4 576 GLN E 624 ASN ** M1838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 72027 Z= 0.230 Angle : 0.496 11.818 97672 Z= 0.257 Chirality : 0.040 0.197 11156 Planarity : 0.004 0.062 12268 Dihedral : 9.978 144.276 10138 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.25 % Allowed : 12.18 % Favored : 86.57 % 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: 0.15 (0.10), residues: 8553 helix: 1.45 (0.09), residues: 3677 sheet: -1.21 (0.15), residues: 1319 loop : -0.75 (0.11), residues: 3557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 473 HIS 0.003 0.001 HIS 2 809 PHE 0.017 0.001 PHE 2 271 TYR 0.018 0.001 TYR 5 46 ARG 0.008 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 291 time to evaluate : 6.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 261 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7982 (mmt) REVERT: 4 881 MET cc_start: 0.7945 (pmm) cc_final: 0.7556 (pmm) REVERT: 5 347 THR cc_start: 0.7281 (OUTLIER) cc_final: 0.7077 (p) REVERT: 6 726 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: 7 506 MET cc_start: 0.5624 (ppp) cc_final: 0.5291 (ppp) REVERT: 7 600 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8222 (ptp) REVERT: A 14 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8820 (ttmm) REVERT: B 63 MET cc_start: 0.9387 (mtm) cc_final: 0.8942 (mtp) REVERT: B 144 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8634 (mttm) REVERT: E 362 MET cc_start: 0.9195 (tmm) cc_final: 0.8846 (ttt) REVERT: F 718 TRP cc_start: 0.6045 (m100) cc_final: 0.5576 (m100) REVERT: F 726 MET cc_start: 0.8659 (tpp) cc_final: 0.8353 (tpt) REVERT: F 778 MET cc_start: 0.4169 (mmt) cc_final: 0.3811 (mmm) REVERT: H 707 LEU cc_start: 0.3241 (OUTLIER) cc_final: 0.2960 (mp) REVERT: H 835 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: K 675 TYR cc_start: 0.4352 (OUTLIER) cc_final: 0.3904 (t80) REVERT: M 1322 TRP cc_start: 0.6404 (p90) cc_final: 0.6201 (p90) REVERT: M 1336 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8141 (pp) REVERT: M 1668 MET cc_start: 0.6512 (mpp) cc_final: 0.6222 (mmm) REVERT: M 2107 LEU cc_start: 0.9033 (tt) cc_final: 0.8805 (tp) outliers start: 96 outliers final: 57 residues processed: 376 average time/residue: 0.6428 time to fit residues: 432.9906 Evaluate side-chains 347 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 280 time to evaluate : 6.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 189 VAL Chi-restraints excluded: chain 2 residue 323 VAL Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 341 SER Chi-restraints excluded: chain 5 residue 347 THR Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 7 residue 103 VAL Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 707 LEU Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1336 LEU Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 809 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 478 optimal weight: 4.9990 chunk 613 optimal weight: 0.0570 chunk 475 optimal weight: 0.9990 chunk 706 optimal weight: 6.9990 chunk 468 optimal weight: 0.8980 chunk 836 optimal weight: 4.9990 chunk 523 optimal weight: 3.9990 chunk 510 optimal weight: 0.6980 chunk 386 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 757 HIS ** 4 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN E 374 GLN E 624 ASN H 555 GLN H 601 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 72027 Z= 0.162 Angle : 0.478 12.354 97672 Z= 0.247 Chirality : 0.039 0.174 11156 Planarity : 0.003 0.061 12268 Dihedral : 9.853 144.485 10135 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.09 % Allowed : 12.60 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.10), residues: 8553 helix: 1.54 (0.09), residues: 3696 sheet: -1.14 (0.15), residues: 1336 loop : -0.69 (0.11), residues: 3521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 473 HIS 0.018 0.001 HIS 7 538 PHE 0.012 0.001 PHE 6 343 TYR 0.032 0.001 TYR 4 753 ARG 0.008 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 294 time to evaluate : 6.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 749 MET cc_start: 0.7896 (ptp) cc_final: 0.6749 (ptp) REVERT: 4 881 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7585 (pmm) REVERT: 6 168 MET cc_start: 0.8071 (tpp) cc_final: 0.7685 (mmm) REVERT: 7 402 MET cc_start: 0.8121 (tpt) cc_final: 0.7865 (tpt) REVERT: 7 506 MET cc_start: 0.5471 (ppp) cc_final: 0.5162 (ppp) REVERT: 7 600 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8149 (ptp) REVERT: A 14 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8831 (ttmm) REVERT: B 63 MET cc_start: 0.9329 (mtm) cc_final: 0.9102 (mtp) REVERT: B 144 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8539 (mttm) REVERT: E 73 GLN cc_start: 0.8571 (tt0) cc_final: 0.8253 (tt0) REVERT: E 362 MET cc_start: 0.9220 (tmm) cc_final: 0.8795 (ttt) REVERT: F 726 MET cc_start: 0.8705 (tpp) cc_final: 0.8408 (tpt) REVERT: F 778 MET cc_start: 0.4618 (mmt) cc_final: 0.4161 (mmm) REVERT: H 477 MET cc_start: 0.6051 (mpp) cc_final: 0.5355 (mpp) REVERT: H 707 LEU cc_start: 0.3164 (OUTLIER) cc_final: 0.2890 (mp) REVERT: H 835 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8140 (mm-30) REVERT: K 675 TYR cc_start: 0.4381 (OUTLIER) cc_final: 0.3949 (t80) REVERT: M 1336 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8079 (pp) REVERT: M 1535 MET cc_start: 0.5617 (pmm) cc_final: 0.5170 (pmm) REVERT: M 2107 LEU cc_start: 0.9016 (tt) cc_final: 0.8809 (tp) outliers start: 84 outliers final: 57 residues processed: 366 average time/residue: 0.6349 time to fit residues: 413.1308 Evaluate side-chains 345 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 280 time to evaluate : 6.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 303 ILE Chi-restraints excluded: chain 2 residue 323 VAL Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 343 THR Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 652 THR Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 4 residue 881 MET Chi-restraints excluded: chain 4 residue 916 VAL Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 300 ILE Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain H residue 707 LEU Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1336 LEU Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 517 optimal weight: 0.9990 chunk 334 optimal weight: 0.9980 chunk 499 optimal weight: 0.7980 chunk 252 optimal weight: 0.5980 chunk 164 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 531 optimal weight: 5.9990 chunk 569 optimal weight: 6.9990 chunk 413 optimal weight: 0.0370 chunk 77 optimal weight: 3.9990 chunk 657 optimal weight: 20.0000 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN ** 4 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 359 GLN ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 72027 Z= 0.159 Angle : 0.484 16.033 97672 Z= 0.249 Chirality : 0.039 0.182 11156 Planarity : 0.003 0.062 12268 Dihedral : 9.787 144.493 10133 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.18 % Allowed : 12.88 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.10), residues: 8553 helix: 1.60 (0.09), residues: 3697 sheet: -1.09 (0.15), residues: 1335 loop : -0.67 (0.11), residues: 3521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP E 473 HIS 0.016 0.001 HIS 7 538 PHE 0.012 0.001 PHE 6 343 TYR 0.026 0.001 TYR 4 753 ARG 0.013 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 293 time to evaluate : 6.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 261 MET cc_start: 0.8080 (mmt) cc_final: 0.7852 (mmt) REVERT: 4 749 MET cc_start: 0.8116 (ptp) cc_final: 0.7114 (ptp) REVERT: 4 881 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7603 (pmm) REVERT: 6 168 MET cc_start: 0.8047 (tpp) cc_final: 0.7627 (mmm) REVERT: 7 456 VAL cc_start: 0.9278 (p) cc_final: 0.9076 (p) REVERT: 7 506 MET cc_start: 0.5449 (ppp) cc_final: 0.5176 (ppp) REVERT: 7 600 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8121 (ptp) REVERT: A 14 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8817 (ttmm) REVERT: B 63 MET cc_start: 0.9325 (mtm) cc_final: 0.8766 (mtp) REVERT: B 144 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8567 (mttm) REVERT: C 5 ASP cc_start: 0.8531 (t0) cc_final: 0.8142 (t0) REVERT: E 73 GLN cc_start: 0.8556 (tt0) cc_final: 0.8262 (tt0) REVERT: E 362 MET cc_start: 0.9269 (tmm) cc_final: 0.8888 (ttt) REVERT: F 726 MET cc_start: 0.8706 (tpp) cc_final: 0.8422 (tpt) REVERT: F 778 MET cc_start: 0.4626 (mmt) cc_final: 0.4171 (mmm) REVERT: G 726 MET cc_start: 0.2824 (ttt) cc_final: 0.2596 (ttp) REVERT: H 477 MET cc_start: 0.6138 (mpp) cc_final: 0.5410 (mpp) REVERT: H 707 LEU cc_start: 0.3169 (OUTLIER) cc_final: 0.2893 (mp) REVERT: H 835 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8138 (mm-30) REVERT: K 675 TYR cc_start: 0.4393 (OUTLIER) cc_final: 0.3966 (t80) REVERT: M 2107 LEU cc_start: 0.9005 (tt) cc_final: 0.8802 (tp) outliers start: 91 outliers final: 63 residues processed: 369 average time/residue: 0.6471 time to fit residues: 428.7312 Evaluate side-chains 357 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 287 time to evaluate : 6.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 303 ILE Chi-restraints excluded: chain 2 residue 323 VAL Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 652 THR Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 867 ARG Chi-restraints excluded: chain 4 residue 881 MET Chi-restraints excluded: chain 4 residue 916 VAL Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 300 ILE Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 335 SER Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 477 VAL Chi-restraints excluded: chain 6 residue 398 THR Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain H residue 707 LEU Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1423 VAL Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 761 optimal weight: 0.0070 chunk 801 optimal weight: 0.0060 chunk 731 optimal weight: 5.9990 chunk 779 optimal weight: 6.9990 chunk 469 optimal weight: 0.9990 chunk 339 optimal weight: 10.0000 chunk 612 optimal weight: 0.6980 chunk 239 optimal weight: 0.5980 chunk 704 optimal weight: 30.0000 chunk 737 optimal weight: 5.9990 chunk 776 optimal weight: 10.0000 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 848 ASN 5 359 GLN ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 72027 Z= 0.137 Angle : 0.483 19.374 97672 Z= 0.247 Chirality : 0.039 0.159 11156 Planarity : 0.003 0.062 12268 Dihedral : 9.721 144.826 10133 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.97 % Allowed : 13.30 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 8553 helix: 1.68 (0.09), residues: 3687 sheet: -1.06 (0.15), residues: 1340 loop : -0.63 (0.11), residues: 3526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP E 473 HIS 0.004 0.000 HIS 3 712 PHE 0.012 0.001 PHE 6 343 TYR 0.025 0.001 TYR 4 753 ARG 0.008 0.000 ARG 2 749 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 304 time to evaluate : 6.382 Fit side-chains revert: symmetry clash REVERT: 3 261 MET cc_start: 0.8030 (mmt) cc_final: 0.7786 (mmt) REVERT: 4 881 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7616 (pmm) REVERT: 6 168 MET cc_start: 0.8058 (tpp) cc_final: 0.7645 (mmm) REVERT: 7 456 VAL cc_start: 0.9263 (p) cc_final: 0.9060 (p) REVERT: 7 506 MET cc_start: 0.5413 (ppp) cc_final: 0.5138 (ppp) REVERT: 7 600 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8016 (ptp) REVERT: A 14 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8797 (ttmm) REVERT: B 63 MET cc_start: 0.9261 (mtm) cc_final: 0.8637 (mtp) REVERT: B 144 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8541 (mttm) REVERT: C 5 ASP cc_start: 0.8522 (t0) cc_final: 0.8122 (t0) REVERT: E 73 GLN cc_start: 0.8553 (tt0) cc_final: 0.8247 (tt0) REVERT: F 726 MET cc_start: 0.8697 (tpp) cc_final: 0.8413 (tpt) REVERT: F 778 MET cc_start: 0.4585 (mmt) cc_final: 0.4128 (mmm) REVERT: G 726 MET cc_start: 0.2920 (ttt) cc_final: 0.2635 (ttp) REVERT: H 477 MET cc_start: 0.6215 (mpp) cc_final: 0.5532 (mpp) REVERT: H 707 LEU cc_start: 0.3177 (OUTLIER) cc_final: 0.2918 (mp) REVERT: H 835 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: K 675 TYR cc_start: 0.4410 (OUTLIER) cc_final: 0.3994 (t80) REVERT: M 1366 MET cc_start: 0.5015 (tpp) cc_final: 0.4405 (mmm) REVERT: M 1423 VAL cc_start: 0.7102 (OUTLIER) cc_final: 0.6603 (p) REVERT: M 2107 LEU cc_start: 0.9018 (tt) cc_final: 0.8791 (tp) outliers start: 75 outliers final: 58 residues processed: 366 average time/residue: 0.6265 time to fit residues: 411.1057 Evaluate side-chains 355 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 289 time to evaluate : 6.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 303 ILE Chi-restraints excluded: chain 2 residue 323 VAL Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 343 THR Chi-restraints excluded: chain 3 residue 425 THR Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 652 THR Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 881 MET Chi-restraints excluded: chain 4 residue 916 VAL Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 300 ILE Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 435 LEU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain H residue 707 LEU Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1423 VAL Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 511 optimal weight: 2.9990 chunk 824 optimal weight: 9.9990 chunk 503 optimal weight: 1.9990 chunk 391 optimal weight: 5.9990 chunk 573 optimal weight: 0.2980 chunk 864 optimal weight: 0.7980 chunk 795 optimal weight: 2.9990 chunk 688 optimal weight: 8.9990 chunk 71 optimal weight: 0.0270 chunk 531 optimal weight: 5.9990 chunk 422 optimal weight: 1.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 359 GLN ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 683 GLN E 624 ASN ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 72027 Z= 0.195 Angle : 0.493 13.767 97672 Z= 0.253 Chirality : 0.040 0.172 11156 Planarity : 0.003 0.062 12268 Dihedral : 9.727 144.223 10129 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.97 % Allowed : 13.36 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 8553 helix: 1.68 (0.09), residues: 3684 sheet: -1.06 (0.15), residues: 1348 loop : -0.64 (0.11), residues: 3521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP E 473 HIS 0.003 0.001 HIS 2 809 PHE 0.012 0.001 PHE 6 343 TYR 0.024 0.001 TYR 4 753 ARG 0.018 0.000 ARG 2 749 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17106 Ramachandran restraints generated. 8553 Oldfield, 0 Emsley, 8553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 292 time to evaluate : 6.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 261 MET cc_start: 0.8106 (mmt) cc_final: 0.7846 (mmt) REVERT: 4 881 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7642 (pmm) REVERT: 7 456 VAL cc_start: 0.9258 (p) cc_final: 0.9051 (p) REVERT: 7 506 MET cc_start: 0.5524 (ppp) cc_final: 0.5250 (ppp) REVERT: 7 600 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.7957 (ptp) REVERT: A 14 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8822 (ttmm) REVERT: B 63 MET cc_start: 0.9317 (mtm) cc_final: 0.8745 (mtp) REVERT: B 144 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8593 (mttm) REVERT: C 5 ASP cc_start: 0.8548 (t0) cc_final: 0.8128 (t0) REVERT: E 73 GLN cc_start: 0.8560 (tt0) cc_final: 0.8254 (tt0) REVERT: F 726 MET cc_start: 0.8700 (tpp) cc_final: 0.8414 (tpt) REVERT: F 778 MET cc_start: 0.4576 (mmt) cc_final: 0.4131 (mmm) REVERT: G 726 MET cc_start: 0.2819 (ttt) cc_final: 0.2548 (ttp) REVERT: H 477 MET cc_start: 0.6097 (mpp) cc_final: 0.5320 (mpp) REVERT: H 707 LEU cc_start: 0.3201 (OUTLIER) cc_final: 0.2928 (mp) REVERT: H 835 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: K 675 TYR cc_start: 0.4413 (OUTLIER) cc_final: 0.4003 (t80) REVERT: M 1366 MET cc_start: 0.4998 (tpp) cc_final: 0.4362 (mmm) REVERT: M 1423 VAL cc_start: 0.7109 (OUTLIER) cc_final: 0.6640 (p) REVERT: M 1535 MET cc_start: 0.5675 (pmm) cc_final: 0.5379 (pmm) REVERT: M 2107 LEU cc_start: 0.9030 (tt) cc_final: 0.8800 (tp) outliers start: 75 outliers final: 64 residues processed: 356 average time/residue: 0.6396 time to fit residues: 407.5741 Evaluate side-chains 360 residues out of total 7817 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 288 time to evaluate : 6.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 188 ASN Chi-restraints excluded: chain 2 residue 303 ILE Chi-restraints excluded: chain 2 residue 323 VAL Chi-restraints excluded: chain 2 residue 388 VAL Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 292 VAL Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 314 LEU Chi-restraints excluded: chain 3 residue 343 THR Chi-restraints excluded: chain 3 residue 425 THR Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 495 VAL Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 582 VAL Chi-restraints excluded: chain 3 residue 652 THR Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 705 VAL Chi-restraints excluded: chain 4 residue 707 LEU Chi-restraints excluded: chain 4 residue 881 MET Chi-restraints excluded: chain 4 residue 916 VAL Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 300 ILE Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 6 residue 266 SER Chi-restraints excluded: chain 6 residue 459 VAL Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 435 LEU Chi-restraints excluded: chain 7 residue 440 VAL Chi-restraints excluded: chain 7 residue 600 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 757 VAL Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 590 VAL Chi-restraints excluded: chain G residue 612 THR Chi-restraints excluded: chain H residue 514 THR Chi-restraints excluded: chain H residue 629 HIS Chi-restraints excluded: chain H residue 707 LEU Chi-restraints excluded: chain H residue 729 TRP Chi-restraints excluded: chain H residue 835 GLU Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain K residue 368 THR Chi-restraints excluded: chain K residue 487 LEU Chi-restraints excluded: chain K residue 675 TYR Chi-restraints excluded: chain M residue 1423 VAL Chi-restraints excluded: chain M residue 1810 ASP Chi-restraints excluded: chain M residue 1816 LEU Chi-restraints excluded: chain M residue 1859 VAL Chi-restraints excluded: chain M residue 1889 VAL Chi-restraints excluded: chain M residue 2102 VAL Chi-restraints excluded: chain N residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 868 random chunks: chunk 546 optimal weight: 6.9990 chunk 733 optimal weight: 20.0000 chunk 210 optimal weight: 0.9980 chunk 634 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 689 optimal weight: 3.9990 chunk 288 optimal weight: 0.0020 chunk 708 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 359 GLN ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN G 725 ASN K 537 ASN ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.131402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.079778 restraints weight = 160716.257| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.12 r_work: 0.3062 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 72027 Z= 0.240 Angle : 0.508 13.178 97672 Z= 0.260 Chirality : 0.040 0.189 11156 Planarity : 0.004 0.062 12268 Dihedral : 9.778 143.492 10129 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.05 % Allowed : 13.46 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.10), residues: 8553 helix: 1.64 (0.09), residues: 3683 sheet: -1.05 (0.14), residues: 1351 loop : -0.66 (0.11), residues: 3519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.001 TRP E 473 HIS 0.004 0.001 HIS 2 809 PHE 0.016 0.001 PHE 2 271 TYR 0.026 0.001 TYR 5 730 ARG 0.016 0.000 ARG 2 749 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12962.44 seconds wall clock time: 256 minutes 45.48 seconds (15405.48 seconds total)