Starting phenix.real_space_refine on Sat Dec 9 15:17:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg8_37213/12_2023/8kg8_37213_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg8_37213/12_2023/8kg8_37213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg8_37213/12_2023/8kg8_37213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg8_37213/12_2023/8kg8_37213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg8_37213/12_2023/8kg8_37213_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg8_37213/12_2023/8kg8_37213_updated.pdb" } resolution = 4.23 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= 0.040 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 38 5.49 5 Mg 5 5.21 5 S 287 5.16 5 C 40440 2.51 5 N 10896 2.21 5 O 12156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 481": "OE1" <-> "OE2" Residue "5 GLU 759": "OE1" <-> "OE2" Residue "6 PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 709": "OD1" <-> "OD2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 626": "OE1" <-> "OE2" Residue "F PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 1881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 2207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 63829 Number of models: 1 Model: "" Number of chains: 25 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: 5503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5503 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 23, 'TRANS': 673} 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: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} 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 91.581 160.591 137.576 1.00250.57 S ATOM 1334 SG CYS 2 344 92.389 164.084 137.802 1.00251.15 S ATOM 1492 SG CYS 2 364 94.913 160.439 138.719 1.00290.84 S ATOM 11648 SG CYS 4 349 104.028 156.934 175.174 1.00350.18 S ATOM 11669 SG CYS 4 352 107.295 157.715 176.962 1.00342.92 S ATOM 11816 SG CYS 4 371 104.003 158.634 178.580 1.00318.84 S ATOM 11858 SG CYS 4 376 105.315 160.483 175.427 1.00330.05 S ATOM 16893 SG CYS 5 183 66.756 160.436 138.520 1.00147.82 S ATOM 16918 SG CYS 5 186 65.162 163.736 138.383 1.00171.38 S ATOM 17082 SG CYS 5 211 68.999 163.699 138.682 1.00157.34 S ATOM 17119 SG CYS 5 236 67.042 162.656 141.580 1.00175.82 S ATOM 22315 SG CYS 6 311 108.580 158.676 151.903 1.00217.40 S ATOM 22337 SG CYS 6 314 108.780 162.347 151.610 1.00227.77 S ATOM 22494 SG CYS 6 333 108.097 160.683 155.180 1.00237.18 S ATOM 22528 SG CYS 6 338 105.507 160.705 152.510 1.00241.86 S ATOM 27560 SG CYS 7 262 76.562 156.169 182.939 1.00239.38 S ATOM 27733 SG CYS 7 284 74.842 158.228 182.207 1.00273.36 S ATOM 27770 SG CYS 7 289 76.893 160.493 181.745 1.00295.63 S ATOM 58502 SG CYS M2108 96.615 48.289 68.893 1.00202.50 S ATOM 58529 SG CYS M2111 98.151 45.719 71.122 1.00195.40 S ATOM 58678 SG CYS M2130 99.474 49.259 71.254 1.00182.05 S ATOM 58702 SG CYS M2133 100.225 46.982 68.292 1.00172.75 S ATOM 58965 SG CYS M2164 75.127 77.008 100.357 1.00198.58 S ATOM 58988 SG CYS M2167 74.845 74.668 103.299 1.00185.57 S ATOM 59089 SG CYS M2179 71.689 75.638 101.306 1.00207.17 S ATOM 59102 SG CYS M2181 73.493 78.085 103.629 1.00213.20 S Time building chain proxies: 24.22, per 1000 atoms: 0.38 Number of scatterers: 63829 At special positions: 0 Unit cell: (153.7, 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 287 16.00 P 38 15.00 Mg 5 11.99 O 12156 8.00 N 10896 7.00 C 40440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.39 Conformation dependent library (CDL) restraints added in 8.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 344 " pdb=" ZN 41400 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 371 " pdb=" ZN 5 801 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 236 " 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 5 211 " pdb=" ZN 61101 " 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 6 314 " 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 M2133 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2130 " 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 M2167 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2164 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2179 " Number of angles added : 30 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 281 helices and 81 sheets defined 38.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.40 Creating SS restraints... Processing helix chain '2' and resid 183 through 187 Processing helix chain '2' and resid 194 through 198 Processing helix chain '2' and resid 201 through 217 Processing helix chain '2' and resid 226 through 237 Processing helix chain '2' and resid 246 through 251 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 264 through 282 removed outlier: 4.154A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 288 No H-bonds generated for 'chain '2' and resid 286 through 288' Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 478 through 488 Processing helix chain '2' and resid 493 through 499 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 573 through 577 removed outlier: 3.708A pdb=" N THR 2 577 " --> pdb=" O ALA 2 573 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 573 through 577' Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 614 through 625 removed outlier: 3.973A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE 2 620 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N HIS 2 621 " --> pdb=" O ARG 2 617 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU 2 622 " --> pdb=" O THR 2 618 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA 2 623 " --> pdb=" O SER 2 619 " (cutoff:3.500A) Processing helix chain '2' and resid 653 through 655 No H-bonds generated for 'chain '2' and resid 653 through 655' Processing helix chain '2' and resid 671 through 676 Processing helix chain '2' and resid 689 through 705 Processing helix chain '2' and resid 740 through 753 Processing helix chain '2' and resid 760 through 773 removed outlier: 3.834A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 783 through 798 Processing helix chain '2' and resid 807 through 823 removed outlier: 3.532A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 848 Processing helix chain '2' and resid 851 through 863 removed outlier: 4.088A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 34 Processing helix chain '3' and resid 36 through 54 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 122 through 136 Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 355 removed outlier: 3.620A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 367 Processing helix chain '3' and resid 375 through 385 Processing helix chain '3' and resid 415 through 425 Processing helix chain '3' and resid 439 through 442 No H-bonds generated for 'chain '3' and resid 439 through 442' Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 492 removed outlier: 3.592A pdb=" N VAL 3 484 " --> pdb=" O ASP 3 480 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE 3 486 " --> pdb=" O ASP 3 482 " (cutoff:3.500A) Processing helix chain '3' and resid 537 through 541 Processing helix chain '3' and resid 556 through 569 Processing helix chain '3' and resid 653 through 666 Processing helix chain '3' and resid 673 through 687 removed outlier: 3.749A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 691 through 693 No H-bonds generated for 'chain '3' and resid 691 through 693' Processing helix chain '3' and resid 699 through 715 Processing helix chain '3' and resid 723 through 737 Processing helix chain '4' and resid 187 through 198 Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 255 through 263 Processing helix chain '4' and resid 265 through 286 Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 314 through 316 No H-bonds generated for 'chain '4' and resid 314 through 316' Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 386 through 388 No H-bonds generated for 'chain '4' and resid 386 through 388' Processing helix chain '4' and resid 503 through 514 Processing helix chain '4' and resid 516 through 526 removed outlier: 4.617A pdb=" N TYR 4 519 " --> pdb=" O GLU 4 516 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 572 through 584 removed outlier: 3.795A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 610 through 612 No H-bonds generated for 'chain '4' and resid 610 through 612' Processing helix chain '4' and resid 639 through 650 Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 700 Processing helix chain '4' and resid 714 through 730 removed outlier: 3.507A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) Processing helix chain '4' and resid 746 through 757 removed outlier: 3.548A pdb=" N MET 4 749 " --> pdb=" O PHE 4 746 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE 4 751 " --> pdb=" O THR 4 748 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS 4 757 " --> pdb=" O ALA 4 754 " (cutoff:3.500A) Processing helix chain '4' and resid 764 through 781 Processing helix chain '4' and resid 795 through 813 removed outlier: 4.878A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU 4 813 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) Processing helix chain '4' and resid 819 through 836 Processing helix chain '4' and resid 852 through 873 removed outlier: 4.378A pdb=" N ILE 4 857 " --> pdb=" O GLY 4 853 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU 4 863 " --> pdb=" O ARG 4 859 " (cutoff:3.500A) Processing helix chain '4' and resid 883 through 888 Processing helix chain '4' and resid 901 through 912 Processing helix chain '5' and resid 21 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 102 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 148 through 150 No H-bonds generated for 'chain '5' and resid 148 through 150' Processing helix chain '5' and resid 262 through 264 No H-bonds generated for 'chain '5' and resid 262 through 264' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 340 through 343 No H-bonds generated for 'chain '5' and resid 340 through 343' Processing helix chain '5' and resid 351 through 362 Processing helix chain '5' and resid 366 through 372 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 446 through 449 No H-bonds generated for 'chain '5' and resid 446 through 449' Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 482 through 484 No H-bonds generated for 'chain '5' and resid 482 through 484' Processing helix chain '5' and resid 487 through 498 removed outlier: 3.563A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS 5 494 " --> pdb=" O ARG 5 490 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 536 through 539 No H-bonds generated for 'chain '5' and resid 536 through 539' Processing helix chain '5' and resid 544 through 549 removed outlier: 3.592A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 579 through 590 removed outlier: 3.970A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) Processing helix chain '5' and resid 596 through 609 Processing helix chain '5' and resid 616 through 640 Processing helix chain '5' and resid 650 through 666 Processing helix chain '5' and resid 674 through 692 removed outlier: 3.843A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) Processing helix chain '5' and resid 708 through 721 Processing helix chain '5' and resid 730 through 736 Processing helix chain '5' and resid 750 through 758 Processing helix chain '6' and resid 106 through 120 Processing helix chain '6' and resid 135 through 146 Processing helix chain '6' and resid 155 through 172 removed outlier: 5.012A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN 6 163 " --> pdb=" O SER 6 159 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY 6 164 " --> pdb=" O MET 6 160 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA 6 165 " --> pdb=" O ARG 6 161 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU 6 166 " --> pdb=" O GLU 6 162 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA 6 167 " --> pdb=" O ASN 6 163 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 192 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 407 through 410 No H-bonds generated for 'chain '6' and resid 407 through 410' Processing helix chain '6' and resid 501 through 506 Processing helix chain '6' and resid 510 through 521 Processing helix chain '6' and resid 525 through 532 Processing helix chain '6' and resid 541 through 552 Processing helix chain '6' and resid 581 through 591 Processing helix chain '6' and resid 627 through 630 No H-bonds generated for 'chain '6' and resid 627 through 630' Processing helix chain '6' and resid 646 through 652 removed outlier: 4.027A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE 6 652 " --> pdb=" O ASP 6 648 " (cutoff:3.500A) Processing helix chain '6' and resid 703 through 708 removed outlier: 3.767A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 736 Processing helix chain '6' and resid 748 through 759 removed outlier: 3.562A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR 6 754 " --> pdb=" O GLN 6 750 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 783 Processing helix chain '6' and resid 797 through 813 Processing helix chain '6' and resid 821 through 835 Processing helix chain '7' and resid 14 through 26 Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 82 through 93 Processing helix chain '7' and resid 102 through 106 Processing helix chain '7' and resid 110 through 123 Processing helix chain '7' and resid 138 through 154 removed outlier: 4.059A pdb=" N MET 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 232 through 234 No H-bonds generated for 'chain '7' and resid 232 through 234' Processing helix chain '7' and resid 287 through 292 Processing helix chain '7' and resid 319 through 321 No H-bonds generated for 'chain '7' and resid 319 through 321' Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 364 through 368 Processing helix chain '7' and resid 396 through 407 Processing helix chain '7' and resid 410 through 418 removed outlier: 4.053A pdb=" N ALA 7 415 " --> pdb=" O TYR 7 411 " (cutoff:3.500A) Processing helix chain '7' and resid 426 through 437 Processing helix chain '7' and resid 466 through 476 Processing helix chain '7' and resid 531 through 541 Processing helix chain '7' and resid 580 through 583 No H-bonds generated for 'chain '7' and resid 580 through 583' Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 608 through 622 Processing helix chain '7' and resid 636 through 648 removed outlier: 4.355A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 674 Processing helix chain '7' and resid 680 through 682 No H-bonds generated for 'chain '7' and resid 680 through 682' Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 727 Processing helix chain 'A' and resid 4 through 21 Processing helix chain 'A' and resid 34 through 60 Processing helix chain 'A' and resid 65 through 104 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.505A pdb=" N ASP A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.836A pdb=" N ASN B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 138 through 162 removed outlier: 3.658A pdb=" N GLY B 143 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 Proline residue: B 183 - end of helix removed outlier: 3.527A pdb=" N GLU B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.964A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.547A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 removed outlier: 4.958A pdb=" N LYS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 191 Processing helix chain 'D' and resid 6 through 12 Processing helix chain 'D' and resid 56 through 72 removed outlier: 3.507A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 105 Processing helix chain 'D' and resid 124 through 153 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 171 through 174 No H-bonds generated for 'chain 'D' and resid 171 through 174' Processing helix chain 'D' and resid 177 through 197 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 279 through 288 removed outlier: 4.546A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 19 removed outlier: 4.959A pdb=" N SER E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER E 19 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 100 through 103 No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 148 through 151 No H-bonds generated for 'chain 'E' and resid 148 through 151' Processing helix chain 'E' and resid 153 through 165 Processing helix chain 'E' and resid 224 through 240 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 267 through 280 removed outlier: 3.855A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 302 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 365 removed outlier: 3.721A pdb=" N LYS E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 377 through 379 No H-bonds generated for 'chain 'E' and resid 377 through 379' Processing helix chain 'E' and resid 382 through 394 removed outlier: 6.351A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 399 No H-bonds generated for 'chain 'E' and resid 397 through 399' Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 421 through 434 Processing helix chain 'E' and resid 465 through 484 removed outlier: 3.715A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E 484 " --> pdb=" O SER E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 516 Processing helix chain 'E' and resid 536 through 538 No H-bonds generated for 'chain 'E' and resid 536 through 538' Processing helix chain 'E' and resid 542 through 557 Processing helix chain 'E' and resid 595 through 598 No H-bonds generated for 'chain 'E' and resid 595 through 598' Processing helix chain 'E' and resid 605 through 614 Processing helix chain 'E' and resid 634 through 646 removed outlier: 4.682A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'F' and resid 673 through 679 Processing helix chain 'F' and resid 713 through 715 No H-bonds generated for 'chain 'F' and resid 713 through 715' Processing helix chain 'F' and resid 724 through 731 Processing helix chain 'F' and resid 783 through 788 removed outlier: 4.305A pdb=" N GLU F 788 " --> pdb=" O SER F 784 " (cutoff:3.500A) Processing helix chain 'F' and resid 819 through 842 removed outlier: 3.894A pdb=" N GLU F 824 " --> pdb=" O SER F 820 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU F 842 " --> pdb=" O THR F 838 " (cutoff:3.500A) Processing helix chain 'F' and resid 851 through 876 removed outlier: 3.502A pdb=" N ASP F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 879 through 888 removed outlier: 3.619A pdb=" N HIS F 887 " --> pdb=" O LEU F 883 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU F 888 " --> pdb=" O SER F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 892 through 904 Processing helix chain 'F' and resid 908 through 923 removed outlier: 3.791A pdb=" N LYS F 912 " --> pdb=" O PRO F 908 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 913 " --> pdb=" O SER F 909 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU F 923 " --> pdb=" O GLU F 919 " (cutoff:3.500A) Processing helix chain 'G' and resid 674 through 679 Processing helix chain 'G' and resid 724 through 732 removed outlier: 4.267A pdb=" N SER G 732 " --> pdb=" O ILE G 728 " (cutoff:3.500A) Processing helix chain 'G' and resid 783 through 786 No H-bonds generated for 'chain 'G' and resid 783 through 786' Processing helix chain 'G' and resid 819 through 843 removed outlier: 3.979A pdb=" N GLU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU G 835 " --> pdb=" O LYS G 831 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR G 840 " --> pdb=" O LEU G 836 " (cutoff:3.500A) Processing helix chain 'G' and resid 851 through 876 Processing helix chain 'G' and resid 879 through 888 removed outlier: 3.916A pdb=" N GLU G 888 " --> pdb=" O SER G 884 " (cutoff:3.500A) Processing helix chain 'G' and resid 892 through 902 Processing helix chain 'G' and resid 908 through 921 removed outlier: 3.579A pdb=" N LYS G 912 " --> pdb=" O PRO G 908 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 913 " --> pdb=" O SER G 909 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE G 914 " --> pdb=" O LEU G 910 " (cutoff:3.500A) Processing helix chain 'H' and resid 674 through 679 Processing helix chain 'H' and resid 724 through 732 removed outlier: 4.248A pdb=" N TRP H 729 " --> pdb=" O ASN H 725 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS H 730 " --> pdb=" O MET H 726 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER H 732 " --> pdb=" O ILE H 728 " (cutoff:3.500A) Processing helix chain 'H' and resid 819 through 842 removed outlier: 3.709A pdb=" N GLU H 824 " --> pdb=" O SER H 820 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU H 835 " --> pdb=" O LYS H 831 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU H 836 " --> pdb=" O VAL H 832 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR H 840 " --> pdb=" O LEU H 836 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU H 841 " --> pdb=" O LEU H 837 " (cutoff:3.500A) Processing helix chain 'H' and resid 851 through 875 Processing helix chain 'H' and resid 879 through 887 Processing helix chain 'H' and resid 892 through 904 Processing helix chain 'H' and resid 908 through 922 Processing helix chain 'M' and resid 1377 through 1379 No H-bonds generated for 'chain 'M' and resid 1377 through 1379' Processing helix chain 'M' and resid 1409 through 1411 No H-bonds generated for 'chain 'M' and resid 1409 through 1411' Processing helix chain 'M' and resid 1437 through 1441 Processing helix chain 'M' and resid 1452 through 1461 removed outlier: 3.604A pdb=" N GLN M1460 " --> pdb=" O GLY M1456 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN M1461 " --> pdb=" O LYS M1457 " (cutoff:3.500A) Processing helix chain 'M' and resid 1525 through 1546 removed outlier: 4.406A pdb=" N MET M1535 " --> pdb=" O ILE M1531 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS M1538 " --> pdb=" O GLN M1534 " (cutoff:3.500A) Processing helix chain 'M' and resid 1566 through 1569 No H-bonds generated for 'chain 'M' and resid 1566 through 1569' Processing helix chain 'M' and resid 1571 through 1583 Processing helix chain 'M' and resid 1598 through 1602 Processing helix chain 'M' and resid 1604 through 1608 Processing helix chain 'M' and resid 1629 through 1640 removed outlier: 3.727A pdb=" N LYS M1634 " --> pdb=" O THR M1630 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU M1635 " --> pdb=" O LEU M1631 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL M1636 " --> pdb=" O LEU M1632 " (cutoff:3.500A) Processing helix chain 'M' and resid 1642 through 1655 removed outlier: 4.006A pdb=" N ILE M1646 " --> pdb=" O SER M1642 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER M1647 " --> pdb=" O GLY M1643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS M1648 " --> pdb=" O SER M1644 " (cutoff:3.500A) Processing helix chain 'M' and resid 1667 through 1682 Processing helix chain 'M' and resid 1701 through 1703 No H-bonds generated for 'chain 'M' and resid 1701 through 1703' Processing helix chain 'M' and resid 1707 through 1713 Processing helix chain 'M' and resid 1739 through 1748 removed outlier: 5.066A pdb=" N ALA M1748 " --> pdb=" O ILE M1744 " (cutoff:3.500A) Processing helix chain 'M' and resid 1785 through 1803 Processing helix chain 'M' and resid 1807 through 1817 Processing helix chain 'M' and resid 1830 through 1854 Processing helix chain 'M' and resid 1876 through 1890 removed outlier: 4.043A pdb=" N TYR M1879 " --> pdb=" O GLU M1876 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA M1880 " --> pdb=" O ASN M1877 " (cutoff:3.500A) Processing helix chain 'M' and resid 1893 through 1895 No H-bonds generated for 'chain 'M' and resid 1893 through 1895' Processing helix chain 'M' and resid 1940 through 1944 Processing helix chain 'M' and resid 1947 through 1975 Proline residue: M1951 - end of helix Processing helix chain 'M' and resid 2003 through 2006 Processing helix chain 'M' and resid 2008 through 2025 Processing helix chain 'M' and resid 2050 through 2062 Processing helix chain 'M' and resid 2069 through 2082 Processing helix chain 'M' and resid 2124 through 2126 No H-bonds generated for 'chain 'M' and resid 2124 through 2126' Processing helix chain 'M' and resid 2139 through 2158 Processing helix chain 'M' and resid 2191 through 2208 Processing helix chain 'M' and resid 2211 through 2220 Processing helix chain 'N' and resid 14 through 29 Proline residue: N 19 - end of helix removed outlier: 3.972A pdb=" N ARG N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 48 Processing helix chain 'N' and resid 56 through 69 Processing helix chain 'N' and resid 80 through 95 Processing helix chain 'N' and resid 166 through 168 No H-bonds generated for 'chain 'N' and resid 166 through 168' Processing helix chain 'N' and resid 175 through 177 No H-bonds generated for 'chain 'N' and resid 175 through 177' Processing helix chain 'N' and resid 211 through 236 removed outlier: 4.771A pdb=" N PHE N 218 " --> pdb=" O LYS N 214 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU N 219 " --> pdb=" O VAL N 215 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG N 221 " --> pdb=" O MET N 217 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN N 234 " --> pdb=" O MET N 230 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE N 235 " --> pdb=" O ARG N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 274 Processing helix chain 'N' and resid 352 through 359 Processing helix chain 'N' and resid 381 through 393 Processing helix chain 'N' and resid 411 through 426 removed outlier: 3.581A pdb=" N ASP N 426 " --> pdb=" O GLN N 422 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 469 Processing helix chain 'N' and resid 510 through 512 No H-bonds generated for 'chain 'N' and resid 510 through 512' Processing helix chain 'N' and resid 514 through 519 Processing helix chain 'N' and resid 546 through 553 Processing helix chain 'N' and resid 595 through 609 Processing sheet with id= A, first strand: chain '2' and resid 241 through 245 removed outlier: 6.722A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL 2 244 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG 2 296 " --> pdb=" O VAL 2 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 405 through 410 removed outlier: 3.768A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN 2 391 " --> pdb=" O VAL 2 324 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL 2 324 " --> pdb=" O GLN 2 391 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 331 through 334 Processing sheet with id= D, first strand: chain '2' and resid 339 through 341 removed outlier: 4.087A pdb=" N ARG 2 374 " --> pdb=" O ASN 2 340 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 679 through 683 removed outlier: 3.692A pdb=" N GLY 2 543 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 578 through 582 Processing sheet with id= G, first strand: chain '2' and resid 628 through 633 Processing sheet with id= H, first strand: chain '3' and resid 95 through 99 removed outlier: 6.775A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER 3 156 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain '3' and resid 165 through 167 removed outlier: 8.419A pdb=" N LEU 3 166 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER 3 181 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 208 through 213 removed outlier: 3.776A pdb=" N ARG 3 208 " --> pdb=" O ALA 3 203 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 273 through 276 removed outlier: 4.057A pdb=" N LYS 3 188 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLN 3 259 " --> pdb=" O VAL 3 186 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 259 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '3' and resid 545 through 549 Processing sheet with id= M, first strand: chain '3' and resid 444 through 448 Processing sheet with id= N, first strand: chain '3' and resid 494 through 499 Processing sheet with id= O, first strand: chain '3' and resid 193 through 198 removed outlier: 6.617A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '4' and resid 414 through 417 removed outlier: 3.892A pdb=" N LYS 4 324 " --> pdb=" O PHE 4 439 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 347 through 349 Processing sheet with id= R, first strand: chain '4' and resid 704 through 707 removed outlier: 6.174A pdb=" N ILE 4 671 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU 4 566 " --> pdb=" O ILE 4 671 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA 4 673 " --> pdb=" O LEU 4 566 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU 4 672 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '4' and resid 604 through 607 Processing sheet with id= T, first strand: chain '4' and resid 653 through 658 Processing sheet with id= U, first strand: chain '4' and resid 916 through 918 Processing sheet with id= V, first strand: chain '4' and resid 339 through 344 removed outlier: 6.710A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '5' and resid 60 through 64 removed outlier: 6.686A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain '5' and resid 325 through 330 removed outlier: 6.537A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 190 through 193 Processing sheet with id= Z, first strand: chain '5' and resid 552 through 556 removed outlier: 6.300A pdb=" N VAL 5 519 " --> pdb=" O VAL 5 412 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU 5 414 " --> pdb=" O VAL 5 519 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA 5 521 " --> pdb=" O LEU 5 414 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N GLY 5 416 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '5' and resid 451 through 455 Processing sheet with id= AB, first strand: chain '5' and resid 501 through 506 Processing sheet with id= AC, first strand: chain '5' and resid 727 through 729 Processing sheet with id= AD, first strand: chain '5' and resid 173 through 178 removed outlier: 6.484A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '6' and resid 150 through 154 removed outlier: 7.259A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain '6' and resid 376 through 382 removed outlier: 6.558A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL 6 400 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA 6 456 " --> pdb=" O VAL 6 400 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE 6 402 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 402 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL 6 404 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE 6 452 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 309 through 311 Processing sheet with id= AH, first strand: chain '6' and resid 571 through 575 removed outlier: 6.532A pdb=" N LEU 6 711 " --> pdb=" O CYS 6 572 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL 6 574 " --> pdb=" O LEU 6 711 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE 6 713 " --> pdb=" O VAL 6 574 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain '6' and resid 595 through 599 removed outlier: 6.562A pdb=" N ILE 6 635 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR 6 598 " --> pdb=" O ILE 6 635 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS 6 637 " --> pdb=" O THR 6 598 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '6' and resid 610 through 614 Processing sheet with id= AK, first strand: chain '6' and resid 660 through 664 Processing sheet with id= AL, first strand: chain '6' and resid 301 through 306 removed outlier: 6.592A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 78 through 81 Processing sheet with id= AN, first strand: chain '7' and resid 330 through 336 removed outlier: 5.311A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 268 through 272 removed outlier: 6.856A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '7' and resid 481 through 484 removed outlier: 6.513A pdb=" N SER 7 562 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE 7 523 " --> pdb=" O SER 7 562 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU 7 564 " --> pdb=" O ILE 7 523 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '7' and resid 545 through 547 Processing sheet with id= AR, first strand: chain 'A' and resid 162 through 166 Processing sheet with id= AS, first strand: chain 'A' and resid 172 through 174 removed outlier: 4.029A pdb=" N GLY A 172 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'B' and resid 24 through 28 Processing sheet with id= AU, first strand: chain 'C' and resid 44 through 47 Processing sheet with id= AV, first strand: chain 'D' and resid 274 through 278 Processing sheet with id= AW, first strand: chain 'D' and resid 246 through 248 Processing sheet with id= AX, first strand: chain 'E' and resid 56 through 61 removed outlier: 7.187A pdb=" N LEU E 27 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL E 59 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER E 80 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE E 30 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU E 82 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER E 32 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL E 84 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP E 119 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU E 83 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR E 121 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'E' and resid 316 through 322 Processing sheet with id= AZ, first strand: chain 'E' and resid 526 through 530 Processing sheet with id= BA, first strand: chain 'E' and resid 578 through 582 Processing sheet with id= BB, first strand: chain 'F' and resid 526 through 529 removed outlier: 3.601A pdb=" N THR F 495 " --> pdb=" O VAL F 502 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR F 504 " --> pdb=" O TYR F 493 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TYR F 493 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 536 through 539 Processing sheet with id= BD, first strand: chain 'F' and resid 581 through 583 removed outlier: 4.083A pdb=" N ARG F 598 " --> pdb=" O VAL F 590 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'F' and resid 637 through 642 removed outlier: 4.069A pdb=" N ALA F 617 " --> pdb=" O VAL F 628 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'F' and resid 703 through 707 removed outlier: 4.293A pdb=" N LEU F 722 " --> pdb=" O LEU F 704 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU F 706 " --> pdb=" O PRO F 720 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'F' and resid 740 through 748 removed outlier: 6.977A pdb=" N ASN F 753 " --> pdb=" O LEU F 745 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU F 747 " --> pdb=" O THR F 751 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR F 751 " --> pdb=" O LEU F 747 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'G' and resid 526 through 528 removed outlier: 3.623A pdb=" N TYR G 526 " --> pdb=" O VAL G 515 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL G 515 " --> pdb=" O TYR G 526 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE G 528 " --> pdb=" O ILE G 513 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE G 513 " --> pdb=" O PHE G 528 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR G 495 " --> pdb=" O VAL G 502 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR G 504 " --> pdb=" O TYR G 493 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR G 493 " --> pdb=" O THR G 504 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 536 through 539 Processing sheet with id= BJ, first strand: chain 'G' and resid 581 through 583 Processing sheet with id= BK, first strand: chain 'G' and resid 615 through 620 removed outlier: 7.117A pdb=" N VAL G 628 " --> pdb=" O VAL G 616 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU G 618 " --> pdb=" O PHE G 626 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE G 626 " --> pdb=" O LEU G 618 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU G 642 " --> pdb=" O TYR G 650 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR G 650 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'G' and resid 742 through 744 Processing sheet with id= BM, first strand: chain 'G' and resid 703 through 707 removed outlier: 3.786A pdb=" N LEU G 722 " --> pdb=" O LEU G 704 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU G 706 " --> pdb=" O PRO G 720 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'H' and resid 526 through 530 removed outlier: 6.002A pdb=" N THR H 504 " --> pdb=" O TYR H 493 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR H 493 " --> pdb=" O THR H 504 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'H' and resid 536 through 540 removed outlier: 3.668A pdb=" N GLY H 543 " --> pdb=" O ASN H 540 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'H' and resid 553 through 556 Processing sheet with id= BQ, first strand: chain 'H' and resid 597 through 600 removed outlier: 3.677A pdb=" N SER H 580 " --> pdb=" O GLY H 591 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'H' and resid 615 through 620 removed outlier: 7.231A pdb=" N VAL H 628 " --> pdb=" O VAL H 616 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU H 618 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE H 626 " --> pdb=" O LEU H 618 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA H 620 " --> pdb=" O ARG H 624 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG H 624 " --> pdb=" O ALA H 620 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU H 642 " --> pdb=" O TYR H 650 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR H 650 " --> pdb=" O GLU H 642 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'H' and resid 772 through 774 removed outlier: 5.700A pdb=" N ILE H 755 " --> pdb=" O PRO H 744 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'M' and resid 1337 through 1341 Processing sheet with id= BU, first strand: chain 'M' and resid 1508 through 1511 removed outlier: 6.407A pdb=" N ASN M1557 " --> pdb=" O ILE M1509 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE M1511 " --> pdb=" O ASN M1557 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU M1559 " --> pdb=" O ILE M1511 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'M' and resid 1590 through 1592 Processing sheet with id= BW, first strand: chain 'M' and resid 1725 through 1727 removed outlier: 3.784A pdb=" N LEU M1909 " --> pdb=" O TYR M1727 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU M1908 " --> pdb=" O LEU M1920 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'M' and resid 1899 through 1906 removed outlier: 3.533A pdb=" N ASP M1899 " --> pdb=" O ASP M1737 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP M1733 " --> pdb=" O LYS M1903 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR M1905 " --> pdb=" O VAL M1731 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL M1731 " --> pdb=" O TYR M1905 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR M1860 " --> pdb=" O LEU M1867 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS M1869 " --> pdb=" O ILE M1858 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE M1858 " --> pdb=" O LYS M1869 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'M' and resid 2162 through 2164 Processing sheet with id= BZ, first strand: chain 'N' and resid 181 through 184 Processing sheet with id= CA, first strand: chain 'N' and resid 325 through 331 removed outlier: 4.855A pdb=" N TRP N 296 " --> pdb=" O ILE N 307 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL N 341 " --> pdb=" O ASP N 308 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU N 329 " --> pdb=" O THR N 342 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N MET N 344 " --> pdb=" O LEU N 327 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU N 327 " --> pdb=" O MET N 344 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'N' and resid 681 through 685 removed outlier: 6.097A pdb=" N LEU N 431 " --> pdb=" O VAL N 400 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR N 480 " --> pdb=" O LEU N 432 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TRP N 434 " --> pdb=" O THR N 480 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE N 482 " --> pdb=" O TRP N 434 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'N' and resid 530 through 532 removed outlier: 6.662A pdb=" N THR N 638 " --> pdb=" O VAL N 540 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE N 542 " --> pdb=" O THR N 638 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL N 640 " --> pdb=" O PHE N 542 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS N 657 " --> pdb=" O MET N 639 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU N 641 " --> pdb=" O LYS N 657 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE N 659 " --> pdb=" O LEU N 641 " (cutoff:3.500A) 2390 hydrogen bonds defined for protein. 6888 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: 26.39 Time building geometry restraints manager: 22.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 21075 1.36 - 1.51: 16781 1.51 - 1.65: 26729 1.65 - 1.80: 270 1.80 - 1.95: 193 Bond restraints: 65048 Sorted by residual: bond pdb=" CA PRO A 157 " pdb=" C PRO A 157 " ideal model delta sigma weight residual 1.517 1.495 0.022 9.30e-03 1.16e+04 5.46e+00 bond pdb=" C VAL 6 300 " pdb=" N ARG 6 301 " ideal model delta sigma weight residual 1.327 1.356 -0.029 1.71e-02 3.42e+03 2.96e+00 bond pdb=" C MET M1610 " pdb=" N PRO M1611 " ideal model delta sigma weight residual 1.331 1.348 -0.017 1.27e-02 6.20e+03 1.86e+00 bond pdb=" C ARG N 18 " pdb=" N PRO N 19 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.75e+00 bond pdb=" CA THR 3 87 " pdb=" CB THR 3 87 " ideal model delta sigma weight residual 1.522 1.540 -0.017 1.32e-02 5.74e+03 1.70e+00 ... (remaining 65043 not shown) Histogram of bond angle deviations from ideal: 95.49 - 103.64: 882 103.64 - 111.79: 31366 111.79 - 119.93: 26198 119.93 - 128.08: 29307 128.08 - 136.23: 383 Bond angle restraints: 88136 Sorted by residual: angle pdb=" N VAL H 780 " pdb=" CA VAL H 780 " pdb=" C VAL H 780 " ideal model delta sigma weight residual 113.42 108.37 5.05 1.17e+00 7.31e-01 1.86e+01 angle pdb=" N ILE 3 197 " pdb=" CA ILE 3 197 " pdb=" C ILE 3 197 " ideal model delta sigma weight residual 113.71 109.65 4.06 9.50e-01 1.11e+00 1.82e+01 angle pdb=" C MET 6 313 " pdb=" N CYS 6 314 " pdb=" CA CYS 6 314 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C SER 5 341 " pdb=" CA SER 5 341 " pdb=" CB SER 5 341 " ideal model delta sigma weight residual 115.89 110.86 5.03 1.32e+00 5.74e-01 1.45e+01 angle pdb=" N ILE M1660 " pdb=" CA ILE M1660 " pdb=" C ILE M1660 " ideal model delta sigma weight residual 112.80 108.45 4.35 1.15e+00 7.56e-01 1.43e+01 ... (remaining 88131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 38830 35.97 - 71.94: 722 71.94 - 107.92: 47 107.92 - 143.89: 3 143.89 - 179.86: 3 Dihedral angle restraints: 39605 sinusoidal: 16293 harmonic: 23312 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 -60.00 119.86 -179.86 1 2.00e+01 2.50e-03 4.80e+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 95.07 -155.07 1 2.00e+01 2.50e-03 4.58e+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 63.21 -123.22 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 39602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 7930 0.048 - 0.095: 1699 0.095 - 0.142: 424 0.142 - 0.190: 12 0.190 - 0.237: 1 Chirality restraints: 10066 Sorted by residual: chirality pdb=" CA MET B 1 " pdb=" N MET B 1 " pdb=" C MET B 1 " pdb=" CB MET B 1 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE G 740 " pdb=" CA ILE G 740 " pdb=" CG1 ILE G 740 " pdb=" CG2 ILE G 740 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CB ILE H 740 " pdb=" CA ILE H 740 " pdb=" CG1 ILE H 740 " pdb=" CG2 ILE H 740 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 10063 not shown) Planarity restraints: 11194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 584 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO G 585 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 585 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 585 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 766 " 0.020 2.00e-02 2.50e+03 1.77e-02 5.45e+00 pdb=" CG PHE F 766 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE F 766 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE F 766 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 766 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 766 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 766 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 661 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO H 662 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 662 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 662 " -0.031 5.00e-02 4.00e+02 ... (remaining 11191 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 885 2.58 - 3.16: 54757 3.16 - 3.74: 106854 3.74 - 4.32: 142927 4.32 - 4.90: 232530 Nonbonded interactions: 537953 Sorted by model distance: nonbonded pdb=" OG SER 7 467 " pdb="MG MG 7 902 " model vdw 1.997 2.170 nonbonded pdb="MG MG 7 902 " pdb=" O2B AGS 7 903 " model vdw 2.025 2.170 nonbonded pdb=" O2B ADP 31001 " pdb="MG MG 31002 " model vdw 2.032 2.170 nonbonded pdb=" O3A AGS 5 802 " pdb="MG MG 5 803 " model vdw 2.035 2.170 nonbonded pdb=" OG SER 5 423 " pdb="MG MG 5 803 " model vdw 2.041 2.170 ... (remaining 537948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 31.360 Check model and map are aligned: 0.770 Set scattering table: 0.430 Process input model: 142.440 Find NCS groups from input model: 3.170 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 65048 Z= 0.144 Angle : 0.578 9.203 88136 Z= 0.323 Chirality : 0.041 0.237 10066 Planarity : 0.004 0.065 11194 Dihedral : 14.463 179.860 24465 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.01 % Allowed : 0.23 % Favored : 99.76 % 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: 0.19 (0.10), residues: 7818 helix: 1.64 (0.09), residues: 3126 sheet: -1.14 (0.14), residues: 1315 loop : -0.74 (0.11), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 50 HIS 0.010 0.001 HIS 7 538 PHE 0.040 0.001 PHE F 766 TYR 0.020 0.001 TYR G 862 ARG 0.006 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 5.771 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.6220 time to fit residues: 217.2789 Evaluate side-chains 184 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 5.800 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 667 optimal weight: 0.2980 chunk 598 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 403 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 chunk 619 optimal weight: 7.9990 chunk 239 optimal weight: 0.6980 chunk 376 optimal weight: 0.4980 chunk 460 optimal weight: 9.9990 chunk 717 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 412 ASN ** 7 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 843 ASN ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 843 ASN ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 291 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 65048 Z= 0.154 Angle : 0.478 8.467 88136 Z= 0.250 Chirality : 0.039 0.158 10066 Planarity : 0.003 0.062 11194 Dihedral : 8.454 151.996 8948 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.62 % 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: 7818 helix: 1.76 (0.09), residues: 3153 sheet: -1.04 (0.14), residues: 1316 loop : -0.69 (0.11), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 473 HIS 0.015 0.001 HIS G 629 PHE 0.032 0.001 PHE F 766 TYR 0.022 0.001 TYR G 862 ARG 0.003 0.000 ARG 2 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 5.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 191 average time/residue: 0.5714 time to fit residues: 197.3207 Evaluate side-chains 184 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 5.809 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5195 time to fit residues: 8.7563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 398 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 597 optimal weight: 30.0000 chunk 488 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 718 optimal weight: 40.0000 chunk 776 optimal weight: 0.8980 chunk 640 optimal weight: 9.9990 chunk 712 optimal weight: 6.9990 chunk 245 optimal weight: 9.9990 chunk 576 optimal weight: 5.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 646 HIS 4 652 GLN ** 4 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 284 ASN 5 344 ASN ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 514 ASN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 ASN ** 7 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 843 ASN F 916 ASN ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 665 ASN H 565 ASN H 665 ASN H 843 ASN ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN M2001 ASN N 13 GLN N 48 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 65048 Z= 0.281 Angle : 0.580 8.978 88136 Z= 0.300 Chirality : 0.040 0.171 10066 Planarity : 0.004 0.061 11194 Dihedral : 8.535 146.970 8948 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.10), residues: 7818 helix: 1.63 (0.09), residues: 3150 sheet: -1.16 (0.14), residues: 1307 loop : -0.75 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 491 HIS 0.016 0.001 HIS 3 253 PHE 0.037 0.002 PHE F 766 TYR 0.023 0.002 TYR G 862 ARG 0.009 0.000 ARG N 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 5.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 192 average time/residue: 0.5989 time to fit residues: 207.0823 Evaluate side-chains 185 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 5.858 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5575 time to fit residues: 9.9859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 710 optimal weight: 9.9990 chunk 540 optimal weight: 9.9990 chunk 372 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 342 optimal weight: 30.0000 chunk 482 optimal weight: 6.9990 chunk 721 optimal weight: 9.9990 chunk 763 optimal weight: 20.0000 chunk 376 optimal weight: 8.9990 chunk 683 optimal weight: 30.0000 chunk 205 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 871 ASN ** 4 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN E 229 GLN E 296 GLN E 342 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 553 GLN F 843 ASN H 843 ASN ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 65048 Z= 0.330 Angle : 0.632 8.888 88136 Z= 0.329 Chirality : 0.041 0.161 10066 Planarity : 0.004 0.062 11194 Dihedral : 8.687 147.965 8948 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % 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: -0.17 (0.10), residues: 7818 helix: 1.28 (0.09), residues: 3146 sheet: -1.30 (0.14), residues: 1319 loop : -0.89 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 743 HIS 0.018 0.001 HIS B 196 PHE 0.038 0.002 PHE F 766 TYR 0.054 0.002 TYR F 651 ARG 0.019 0.001 ARG F 649 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 5.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 188 average time/residue: 0.6070 time to fit residues: 206.2869 Evaluate side-chains 185 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 5.826 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5087 time to fit residues: 9.7087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 635 optimal weight: 5.9990 chunk 433 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 568 optimal weight: 1.9990 chunk 315 optimal weight: 10.0000 chunk 651 optimal weight: 10.0000 chunk 527 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 389 optimal weight: 10.0000 chunk 685 optimal weight: 10.0000 chunk 192 optimal weight: 50.0000 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 760 GLN 2 780 GLN 3 253 HIS ** 3 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 198 ASN ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 258 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN E 402 GLN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 741 HIS F 843 ASN ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 843 ASN ** H 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 666 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 65048 Z= 0.339 Angle : 0.650 14.164 88136 Z= 0.337 Chirality : 0.042 0.279 10066 Planarity : 0.004 0.063 11194 Dihedral : 8.780 148.056 8948 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.10), residues: 7818 helix: 1.11 (0.09), residues: 3149 sheet: -1.29 (0.14), residues: 1316 loop : -0.99 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 3 153 HIS 0.010 0.001 HIS A 33 PHE 0.041 0.002 PHE F 766 TYR 0.031 0.002 TYR F 862 ARG 0.007 0.001 ARG 6 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 5.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.6312 time to fit residues: 208.7677 Evaluate side-chains 183 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 5.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 256 optimal weight: 10.0000 chunk 687 optimal weight: 0.2980 chunk 150 optimal weight: 3.9990 chunk 448 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 764 optimal weight: 10.0000 chunk 634 optimal weight: 5.9990 chunk 353 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 chunk 252 optimal weight: 50.0000 chunk 401 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 653 ASN 3 312 ASN 3 691 ASN ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 506 ASN 6 514 ASN ** 7 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 553 GLN ** F 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 816 GLN F 843 ASN ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 665 ASN ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 843 ASN ** H 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1838 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 65048 Z= 0.168 Angle : 0.530 11.489 88136 Z= 0.274 Chirality : 0.040 0.208 10066 Planarity : 0.004 0.062 11194 Dihedral : 8.572 146.889 8948 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.01 % Allowed : 1.81 % Favored : 98.18 % 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: 0.06 (0.10), residues: 7818 helix: 1.53 (0.09), residues: 3146 sheet: -1.21 (0.14), residues: 1316 loop : -0.82 (0.11), residues: 3356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 491 HIS 0.009 0.001 HIS G 887 PHE 0.037 0.001 PHE M1351 TYR 0.028 0.001 TYR F 862 ARG 0.004 0.000 ARG 3 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 5.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.6287 time to fit residues: 212.8267 Evaluate side-chains 183 residues out of total 7128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 5.807 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.1841 > 50: distance: 106 - 122: 10.541 distance: 117 - 122: 6.843 distance: 122 - 123: 7.476 distance: 123 - 124: 11.008 distance: 123 - 126: 12.134 distance: 124 - 125: 3.894 distance: 124 - 129: 6.102 distance: 126 - 127: 18.615 distance: 126 - 128: 12.474 distance: 129 - 130: 11.729 distance: 130 - 131: 8.667 distance: 130 - 133: 15.217 distance: 131 - 132: 12.562 distance: 131 - 135: 9.455 distance: 133 - 134: 11.895 distance: 135 - 136: 23.378 distance: 136 - 137: 17.705 distance: 136 - 139: 22.089 distance: 137 - 138: 27.030 distance: 137 - 143: 8.386 distance: 139 - 140: 14.541 distance: 140 - 141: 24.756 distance: 141 - 142: 12.858 distance: 143 - 144: 14.536 distance: 144 - 145: 21.508 distance: 144 - 147: 41.437 distance: 145 - 146: 17.543 distance: 145 - 150: 18.739 distance: 147 - 148: 17.112 distance: 147 - 149: 17.269 distance: 150 - 151: 43.326 distance: 151 - 152: 11.181 distance: 151 - 154: 20.976 distance: 152 - 153: 7.526 distance: 152 - 158: 11.056 distance: 154 - 155: 28.935 distance: 155 - 156: 28.573 distance: 155 - 157: 29.810 distance: 158 - 159: 16.341 distance: 158 - 164: 38.983 distance: 159 - 160: 26.082 distance: 159 - 162: 31.997 distance: 160 - 161: 14.660 distance: 160 - 165: 8.774 distance: 162 - 163: 8.562 distance: 163 - 164: 21.533 distance: 165 - 166: 22.627 distance: 165 - 171: 14.459 distance: 166 - 167: 17.442 distance: 166 - 169: 12.320 distance: 167 - 168: 15.917 distance: 167 - 172: 19.758 distance: 169 - 170: 17.968 distance: 170 - 171: 18.061 distance: 172 - 173: 26.178 distance: 173 - 174: 9.241 distance: 174 - 176: 11.002 distance: 176 - 177: 13.028 distance: 177 - 178: 53.388 distance: 177 - 180: 28.626 distance: 178 - 179: 25.746 distance: 178 - 185: 22.460 distance: 181 - 182: 39.156 distance: 182 - 183: 19.065 distance: 182 - 184: 9.695 distance: 185 - 186: 17.946 distance: 186 - 187: 14.799 distance: 186 - 189: 50.635 distance: 187 - 188: 3.507 distance: 187 - 196: 32.960 distance: 189 - 190: 18.997 distance: 190 - 191: 20.369 distance: 191 - 192: 6.883 distance: 192 - 193: 8.542 distance: 193 - 194: 14.704 distance: 193 - 195: 9.318