Starting phenix.real_space_refine on Sun Apr 7 15:22:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg9_37215/04_2024/8kg9_37215_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg9_37215/04_2024/8kg9_37215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg9_37215/04_2024/8kg9_37215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg9_37215/04_2024/8kg9_37215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg9_37215/04_2024/8kg9_37215_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg9_37215/04_2024/8kg9_37215_updated.pdb" } resolution = 4.52 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= 0.008 sd= 0.054 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 33 5.49 5 Mg 4 5.21 5 S 283 5.16 5 C 40251 2.51 5 N 10862 2.21 5 O 12067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 421": "OD1" <-> "OD2" Residue "4 TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 738": "NH1" <-> "NH2" Residue "6 PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 500": "OD1" <-> "OD2" Residue "7 PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 709": "OD1" <-> "OD2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "E ASP 149": "OD1" <-> "OD2" Residue "E TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 1409": "OE1" <-> "OE2" Residue "M PHE 1536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 506": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 63507 Number of models: 1 Model: "" Number of chains: 25 Chain: "2" Number of atoms: 5270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5270 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 641} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "3" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4948 Classifications: {'peptide': 637} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 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: 5390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5390 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 652} Chain breaks: 8 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "5" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5325 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 649} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "6" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4955 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 605} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4945 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 30, 'TRANS': 605} Chain breaks: 6 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'TYR:plan': 2, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1633 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 196} 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: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1617 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1387 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} 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: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4599 Classifications: {'peptide': 568} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 552} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3380 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3411 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 307 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain breaks: 1 Chain: "J" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 159 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "M" Number of atoms: 6447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6447 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 31, 'TRANS': 780} Chain breaks: 5 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 4199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4199 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 29, 'TRANS': 499} Chain breaks: 5 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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 1339 SG CYS 2 341 88.539 159.415 134.540 1.00361.23 S ATOM 1362 SG CYS 2 344 88.192 163.284 134.982 1.00359.77 S ATOM 1520 SG CYS 2 364 91.650 161.275 134.619 1.00432.54 S ATOM 1541 SG CYS 2 367 89.760 161.337 137.696 1.00426.58 S ATOM 11669 SG CYS 4 349 101.072 155.894 172.964 1.00753.81 S ATOM 11690 SG CYS 4 352 103.538 158.751 172.296 1.00722.63 S ATOM 11837 SG CYS 4 371 99.939 159.112 174.042 1.00756.28 S ATOM 11879 SG CYS 4 376 100.110 159.106 170.623 1.00753.01 S ATOM 16761 SG CYS 5 183 66.266 160.127 133.869 1.00293.23 S ATOM 16786 SG CYS 5 186 64.203 163.370 133.844 1.00313.59 S ATOM 16956 SG CYS 5 211 67.707 163.864 133.724 1.00293.92 S ATOM 16984 SG CYS 5 236 66.476 162.424 136.880 1.00331.27 S ATOM 22369 SG CYS 6 333 101.547 159.733 149.880 1.00484.66 S ATOM 22403 SG CYS 6 338 100.798 163.691 147.854 1.00520.34 S ATOM 27422 SG CYS 7 262 76.546 154.613 178.537 1.00646.02 S ATOM 27445 SG CYS 7 265 74.011 155.717 180.657 1.00624.90 S ATOM 27595 SG CYS 7 284 73.697 156.783 176.980 1.00625.93 S ATOM 27632 SG CYS 7 289 76.188 158.513 178.967 1.00570.45 S ATOM 58722 SG CYS M2164 68.498 73.461 96.578 1.00903.10 S ATOM 58745 SG CYS M2167 67.638 70.863 98.952 1.00961.29 S ATOM 58846 SG CYS M2179 64.963 72.760 97.214 1.00879.63 S ATOM 58859 SG CYS M2181 67.685 74.427 100.068 1.00889.30 S ATOM 58262 SG CYS M2108 86.551 41.827 65.457 1.00999.99 S ATOM 58289 SG CYS M2111 87.470 40.436 68.830 1.00999.99 S ATOM 58438 SG CYS M2130 89.894 42.767 67.105 1.00999.99 S ATOM 58462 SG CYS M2133 89.564 39.418 65.716 1.00999.99 S Time building chain proxies: 24.65, per 1000 atoms: 0.39 Number of scatterers: 63507 At special positions: 0 Unit cell: (152.64, 246.98, 226.84, 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 283 16.00 P 33 15.00 Mg 4 11.99 O 12067 8.00 N 10862 7.00 C 40251 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.90 Conformation dependent library (CDL) restraints added in 8.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 367 " 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 4 371 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 352 " pdb=" ZN 5 802 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 183 " pdb=" ZN 61400 " pdb="ZN ZN 61400 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 61400 " - pdb=" SG CYS 6 338 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 265 " 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 M3000 " pdb="ZN ZN M3000 " - pdb=" SG CYS M2164 " pdb="ZN ZN M3000 " - pdb=" SG CYS M2167 " pdb="ZN ZN M3000 " - pdb=" SG CYS M2179 " pdb="ZN ZN M3000 " - pdb=" SG CYS M2181 " pdb=" ZN M3001 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2130 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2133 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2108 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2111 " Number of angles added : 36 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 263 helices and 67 sheets defined 39.4% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.95 Creating SS restraints... Processing helix chain '2' and resid 183 through 187 Processing helix chain '2' and resid 194 through 199 Processing helix chain '2' and resid 201 through 216 removed outlier: 3.758A pdb=" N LEU 2 216 " --> pdb=" O LYS 2 212 " (cutoff:3.500A) Processing helix chain '2' and resid 226 through 230 Processing helix chain '2' and resid 233 through 237 Processing helix chain '2' and resid 255 through 262 Processing helix chain '2' and resid 264 through 282 Processing helix chain '2' and resid 306 through 308 No H-bonds generated for 'chain '2' and resid 306 through 308' Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 478 through 489 Processing helix chain '2' and resid 493 through 500 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 556 Processing helix chain '2' and resid 573 through 576 No H-bonds generated for 'chain '2' and resid 573 through 576' Processing helix chain '2' and resid 595 through 599 Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 614 through 625 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 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 676 Processing helix chain '2' and resid 689 through 706 Processing helix chain '2' and resid 740 through 754 Processing helix chain '2' and resid 760 through 773 Processing helix chain '2' and resid 783 through 793 Processing helix chain '2' and resid 807 through 824 Processing helix chain '2' and resid 831 through 848 Processing helix chain '2' and resid 851 through 865 removed outlier: 4.172A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR 2 864 " --> pdb=" O SER 2 860 " (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 108 through 116 removed outlier: 3.586A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 137 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 144 through 149 removed outlier: 3.523A pdb=" N SER 3 149 " --> pdb=" O SER 3 145 " (cutoff:3.500A) Processing helix chain '3' and resid 302 through 305 Processing helix chain '3' and resid 344 through 348 Processing helix chain '3' and resid 351 through 355 Processing helix chain '3' and resid 357 through 366 removed outlier: 3.705A pdb=" N PHE 3 360 " --> pdb=" O LYS 3 357 " (cutoff:3.500A) 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 443 Processing helix chain '3' and resid 462 through 465 No H-bonds generated for 'chain '3' and resid 462 through 465' Processing helix chain '3' and resid 480 through 492 removed outlier: 5.086A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 529 through 532 No H-bonds generated for 'chain '3' and resid 529 through 532' Processing helix chain '3' and resid 555 through 570 Processing helix chain '3' and resid 653 through 666 Processing helix chain '3' and resid 673 through 687 removed outlier: 4.289A pdb=" N ASP 3 685 " --> pdb=" O LYS 3 681 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 716 removed outlier: 4.325A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 723 through 738 Processing helix chain '4' and resid 187 through 194 Processing helix chain '4' and resid 218 through 222 Processing helix chain '4' and resid 225 through 234 Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 252 through 263 removed outlier: 3.562A pdb=" N ASP 4 256 " --> pdb=" O LYS 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 286 removed outlier: 3.893A pdb=" N VAL 4 285 " --> pdb=" O VAL 4 281 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 506 through 514 Processing helix chain '4' and resid 516 through 525 removed outlier: 4.587A pdb=" N TYR 4 519 " --> pdb=" O GLU 4 516 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER 4 520 " --> pdb=" O ASP 4 517 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU 4 521 " --> pdb=" O LEU 4 518 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU 4 522 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER 4 525 " --> pdb=" O LEU 4 522 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 572 through 584 removed outlier: 3.968A pdb=" N ILE 4 584 " --> pdb=" O TYR 4 580 " (cutoff:3.500A) Processing helix chain '4' and resid 638 through 651 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 Processing helix chain '4' and resid 745 through 757 removed outlier: 4.061A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) Processing helix chain '4' and resid 764 through 779 Processing helix chain '4' and resid 795 through 813 removed outlier: 4.867A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU 4 813 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) Processing helix chain '4' and resid 819 through 834 Processing helix chain '4' and resid 847 through 849 No H-bonds generated for 'chain '4' and resid 847 through 849' Processing helix chain '4' and resid 858 through 875 Processing helix chain '4' and resid 883 through 892 removed outlier: 3.669A pdb=" N ASN 4 891 " --> pdb=" O ILE 4 887 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU 4 892 " --> pdb=" O LYS 4 888 " (cutoff:3.500A) Processing helix chain '4' and resid 900 through 913 Processing helix chain '5' and resid 21 through 36 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 184 through 186 No H-bonds generated for 'chain '5' and resid 184 through 186' Processing helix chain '5' and resid 350 through 362 removed outlier: 3.519A pdb=" N GLU 5 354 " --> pdb=" O THR 5 350 " (cutoff:3.500A) Processing helix chain '5' and resid 364 through 373 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 468 through 472 Processing helix chain '5' and resid 487 through 499 removed outlier: 3.769A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) Processing helix chain '5' and resid 506 through 508 No H-bonds generated for 'chain '5' and resid 506 through 508' 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 550 Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 578 through 591 removed outlier: 3.909A pdb=" N MET 5 583 " --> pdb=" O ASN 5 579 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY 5 591 " --> pdb=" O GLN 5 587 " (cutoff:3.500A) Processing helix chain '5' and resid 596 through 612 Proline residue: 5 612 - end of helix Processing helix chain '5' and resid 618 through 639 removed outlier: 4.011A pdb=" N SER 5 624 " --> pdb=" O GLU 5 620 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL 5 627 " --> pdb=" O SER 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 646 through 649 No H-bonds generated for 'chain '5' and resid 646 through 649' Processing helix chain '5' and resid 651 through 666 removed outlier: 3.613A pdb=" N THR 5 660 " --> pdb=" O ILE 5 656 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA 5 664 " --> pdb=" O THR 5 660 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 693 removed outlier: 4.182A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA 5 692 " --> pdb=" O THR 5 688 " (cutoff:3.500A) Processing helix chain '5' and resid 707 through 722 removed outlier: 3.530A pdb=" N ILE 5 711 " --> pdb=" O LEU 5 708 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG 5 720 " --> pdb=" O GLU 5 717 " (cutoff:3.500A) Processing helix chain '5' and resid 731 through 745 removed outlier: 6.340A pdb=" N PHE 5 737 " --> pdb=" O LEU 5 733 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL 5 738 " --> pdb=" O ARG 5 734 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP 5 739 " --> pdb=" O ARG 5 735 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ARG 5 742 " --> pdb=" O VAL 5 738 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE 5 743 " --> pdb=" O ASP 5 739 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN 5 745 " --> pdb=" O HIS 5 741 " (cutoff:3.500A) Processing helix chain '5' and resid 747 through 758 removed outlier: 4.639A pdb=" N LYS 5 757 " --> pdb=" O TYR 5 753 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS 5 758 " --> pdb=" O ALA 5 754 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 119 removed outlier: 4.837A pdb=" N GLU 6 116 " --> pdb=" O ARG 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 139 through 146 Processing helix chain '6' and resid 155 through 158 No H-bonds generated for 'chain '6' and resid 155 through 158' Processing helix chain '6' and resid 165 through 172 Processing helix chain '6' and resid 179 through 191 removed outlier: 4.939A pdb=" N ARG 6 186 " --> pdb=" O GLN 6 182 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG 6 187 " --> pdb=" O LYS 6 183 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL 6 189 " --> pdb=" O LEU 6 185 " (cutoff:3.500A) Processing helix chain '6' and resid 383 through 388 Processing helix chain '6' and resid 501 through 507 Processing helix chain '6' and resid 510 through 521 Processing helix chain '6' and resid 523 through 532 removed outlier: 4.712A pdb=" N TYR 6 526 " --> pdb=" O GLU 6 523 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP 6 527 " --> pdb=" O HIS 6 524 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS 6 528 " --> pdb=" O ILE 6 525 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU 6 529 " --> pdb=" O TYR 6 526 " (cutoff:3.500A) Processing helix chain '6' and resid 542 through 552 Processing helix chain '6' and resid 581 through 591 Processing helix chain '6' and resid 627 through 631 Processing helix chain '6' and resid 646 through 656 removed outlier: 4.310A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE 6 652 " --> pdb=" O ASP 6 648 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) Processing helix chain '6' and resid 703 through 708 Processing helix chain '6' and resid 723 through 734 removed outlier: 4.382A pdb=" N ALA 6 728 " --> pdb=" O ASP 6 724 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER 6 729 " --> pdb=" O THR 6 725 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL 6 732 " --> pdb=" O ALA 6 728 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP 6 733 " --> pdb=" O SER 6 729 " (cutoff:3.500A) Processing helix chain '6' and resid 748 through 760 Processing helix chain '6' and resid 767 through 783 Processing helix chain '6' and resid 788 through 790 No H-bonds generated for 'chain '6' and resid 788 through 790' Processing helix chain '6' and resid 797 through 809 Processing helix chain '6' and resid 821 through 834 Processing helix chain '7' and resid 14 through 27 Processing helix chain '7' and resid 30 through 33 No H-bonds generated for 'chain '7' and resid 30 through 33' Processing helix chain '7' and resid 62 through 72 Processing helix chain '7' and resid 82 through 95 Processing helix chain '7' and resid 99 through 108 removed outlier: 5.819A pdb=" N VAL 7 103 " --> pdb=" O ASP 7 100 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 123 Processing helix chain '7' and resid 137 through 146 removed outlier: 4.000A pdb=" N ARG 7 146 " --> pdb=" O ILE 7 142 " (cutoff:3.500A) Processing helix chain '7' and resid 194 through 197 No H-bonds generated for 'chain '7' and resid 194 through 197' Processing helix chain '7' and resid 214 through 216 No H-bonds generated for 'chain '7' and resid 214 through 216' 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 293 removed outlier: 4.598A pdb=" N ASN 7 292 " --> pdb=" O GLU 7 288 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN 7 293 " --> pdb=" O CYS 7 289 " (cutoff:3.500A) Processing helix chain '7' and resid 364 through 368 Processing helix chain '7' and resid 398 through 408 removed outlier: 3.769A pdb=" N MET 7 402 " --> pdb=" O GLU 7 398 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 419 removed outlier: 4.135A pdb=" N ALA 7 419 " --> pdb=" O ALA 7 415 " (cutoff:3.500A) Processing helix chain '7' and resid 426 through 437 removed outlier: 3.566A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL 7 437 " --> pdb=" O LEU 7 433 " (cutoff:3.500A) Processing helix chain '7' and resid 472 through 476 removed outlier: 3.699A pdb=" N ILE 7 476 " --> pdb=" O ALA 7 472 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 472 through 476' Processing helix chain '7' and resid 500 through 502 No H-bonds generated for 'chain '7' and resid 500 through 502' Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 531 through 543 Processing helix chain '7' and resid 570 through 572 No H-bonds generated for 'chain '7' and resid 570 through 572' Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 608 through 619 Processing helix chain '7' and resid 635 through 643 Processing helix chain '7' and resid 654 through 672 Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 728 Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.674A pdb=" N GLY A 6 " --> pdb=" O TYR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 60 Processing helix chain 'A' and resid 65 through 104 removed outlier: 3.668A pdb=" N CYS A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 142 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 117 through 133 removed outlier: 4.172A pdb=" N LEU B 120 " --> pdb=" O TRP B 117 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA B 130 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS B 131 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 162 Processing helix chain 'B' and resid 175 through 199 Proline residue: B 183 - end of helix Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 48 through 56 removed outlier: 4.235A 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 114 Processing helix chain 'C' and resid 118 through 140 Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 171 through 192 Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 56 through 72 Processing helix chain 'D' and resid 81 through 106 Processing helix chain 'D' and resid 123 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 201 removed outlier: 5.113A pdb=" N LYS D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) 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 279 through 288 removed outlier: 4.303A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 18 removed outlier: 3.553A pdb=" N SER E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 52 Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 92 through 96 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 135 Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.763A pdb=" N THR E 151 " --> pdb=" O THR E 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 147 through 151' Processing helix chain 'E' and resid 153 through 164 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 283 removed outlier: 4.302A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA E 283 " --> pdb=" O SER E 279 " (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 335 through 339 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 382 through 399 removed outlier: 4.337A pdb=" N GLU E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 removed outlier: 3.686A pdb=" N ILE E 404 " --> pdb=" O LEU E 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 401 through 404' Processing helix chain 'E' and resid 421 through 434 Processing helix chain 'E' and resid 462 through 484 Processing helix chain 'E' and resid 489 through 515 Processing helix chain 'E' and resid 536 through 540 Processing helix chain 'E' and resid 542 through 558 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 604 through 614 Processing helix chain 'E' and resid 634 through 646 removed outlier: 4.373A 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 671 through 679 Processing helix chain 'F' and resid 724 through 732 Processing helix chain 'F' and resid 783 through 790 Processing helix chain 'F' and resid 819 through 843 Processing helix chain 'F' and resid 851 through 876 Processing helix chain 'F' and resid 879 through 888 Processing helix chain 'F' and resid 892 through 905 Processing helix chain 'F' and resid 908 through 922 Processing helix chain 'G' and resid 672 through 679 Processing helix chain 'G' and resid 724 through 734 removed outlier: 5.454A pdb=" N SER G 732 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLY G 733 " --> pdb=" O TRP G 729 " (cutoff:3.500A) Processing helix chain 'G' and resid 783 through 789 Processing helix chain 'G' and resid 819 through 844 Processing helix chain 'G' and resid 851 through 876 Processing helix chain 'G' and resid 879 through 888 removed outlier: 3.515A pdb=" N GLU G 888 " --> pdb=" O SER G 884 " (cutoff:3.500A) Processing helix chain 'G' and resid 892 through 904 Processing helix chain 'G' and resid 908 through 922 Processing helix chain 'H' and resid 671 through 679 Processing helix chain 'H' and resid 724 through 731 Processing helix chain 'H' and resid 783 through 789 Processing helix chain 'H' and resid 819 through 843 Processing helix chain 'H' and resid 851 through 876 Processing helix chain 'H' and resid 879 through 888 Processing helix chain 'H' and resid 892 through 905 Processing helix chain 'H' and resid 908 through 922 Processing helix chain 'M' and resid 1365 through 1368 No H-bonds generated for 'chain 'M' and resid 1365 through 1368' Processing helix chain 'M' and resid 1434 through 1441 Processing helix chain 'M' and resid 1527 through 1538 Processing helix chain 'M' and resid 1540 through 1547 removed outlier: 4.385A pdb=" N THR M1545 " --> pdb=" O GLY M1541 " (cutoff:3.500A) Processing helix chain 'M' and resid 1566 through 1579 Processing helix chain 'M' and resid 1595 through 1604 removed outlier: 4.454A pdb=" N LYS M1599 " --> pdb=" O PRO M1595 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU M1600 " --> pdb=" O PHE M1596 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY M1602 " --> pdb=" O THR M1598 " (cutoff:3.500A) Processing helix chain 'M' and resid 1628 through 1656 removed outlier: 3.537A pdb=" N LYS M1633 " --> pdb=" O PRO M1629 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY M1643 " --> pdb=" O VAL M1639 " (cutoff:3.500A) Processing helix chain 'M' and resid 1669 through 1682 Processing helix chain 'M' and resid 1707 through 1713 removed outlier: 3.793A pdb=" N MET M1713 " --> pdb=" O THR M1709 " (cutoff:3.500A) Processing helix chain 'M' and resid 1739 through 1748 removed outlier: 3.600A pdb=" N ALA M1748 " --> pdb=" O ILE M1744 " (cutoff:3.500A) Processing helix chain 'M' and resid 1785 through 1802 Processing helix chain 'M' and resid 1807 through 1821 removed outlier: 4.040A pdb=" N ALA M1817 " --> pdb=" O VAL M1813 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER M1818 " --> pdb=" O ASN M1814 " (cutoff:3.500A) Processing helix chain 'M' and resid 1830 through 1853 Processing helix chain 'M' and resid 1876 through 1892 removed outlier: 3.700A pdb=" N ALA M1880 " --> pdb=" O GLU M1876 " (cutoff:3.500A) 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 1998 through 2025 removed outlier: 3.519A pdb=" N HIS M2005 " --> pdb=" O ASN M2001 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS M2009 " --> pdb=" O HIS M2005 " (cutoff:3.500A) Proline residue: M2010 - end of helix removed outlier: 3.800A pdb=" N GLU M2024 " --> pdb=" O LYS M2020 " (cutoff:3.500A) Processing helix chain 'M' and resid 2029 through 2035 removed outlier: 3.745A pdb=" N ASP M2034 " --> pdb=" O GLN M2030 " (cutoff:3.500A) Processing helix chain 'M' and resid 2050 through 2064 removed outlier: 3.962A pdb=" N LEU M2064 " --> pdb=" O HIS M2060 " (cutoff:3.500A) Processing helix chain 'M' and resid 2067 through 2082 removed outlier: 4.014A pdb=" N LEU M2070 " --> pdb=" O SER M2067 " (cutoff:3.500A) Processing helix chain 'M' and resid 2124 through 2128 removed outlier: 3.643A pdb=" N PHE M2128 " --> pdb=" O PRO M2124 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 2124 through 2128' Processing helix chain 'M' and resid 2139 through 2159 Processing helix chain 'M' and resid 2191 through 2207 Processing helix chain 'M' and resid 2211 through 2221 Processing helix chain 'N' and resid 14 through 29 Proline residue: N 19 - end of helix removed outlier: 3.879A pdb=" N ARG N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS N 28 " --> pdb=" O VAL N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 47 Processing helix chain 'N' and resid 55 through 69 Processing helix chain 'N' and resid 80 through 97 Processing helix chain 'N' and resid 211 through 236 removed outlier: 3.914A pdb=" N PHE N 218 " --> pdb=" O LYS N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 275 removed outlier: 3.946A pdb=" N LEU N 275 " --> pdb=" O ILE N 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 271 through 275' Processing helix chain 'N' and resid 352 through 359 Processing helix chain 'N' and resid 382 through 393 Processing helix chain 'N' and resid 411 through 426 removed outlier: 3.761A pdb=" N ASP N 426 " --> pdb=" O GLN N 422 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 463 Processing helix chain 'N' and resid 466 through 471 Processing helix chain 'N' and resid 510 through 513 Processing helix chain 'N' and resid 516 through 519 No H-bonds generated for 'chain 'N' and resid 516 through 519' Processing helix chain 'N' and resid 546 through 553 Processing helix chain 'N' and resid 595 through 609 Processing helix chain 'N' and resid 627 through 630 No H-bonds generated for 'chain 'N' and resid 627 through 630' Processing sheet with id= A, first strand: chain '2' and resid 317 through 319 removed outlier: 3.791A pdb=" N LYS 2 457 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR 2 427 " --> pdb=" O SER 2 455 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 2 455 " --> pdb=" O THR 2 427 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 339 through 341 Processing sheet with id= C, first strand: chain '2' and resid 385 through 389 Processing sheet with id= D, first strand: chain '2' and resid 525 through 527 Processing sheet with id= E, first strand: chain '2' and resid 679 through 682 removed outlier: 7.840A pdb=" N VAL 2 539 " --> pdb=" O CYS 2 644 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE 2 646 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU 2 541 " --> pdb=" O ILE 2 646 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA 2 648 " --> pdb=" O LEU 2 541 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY 2 602 " --> pdb=" O SER 2 645 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE 2 647 " --> pdb=" O GLY 2 602 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 579 through 583 Processing sheet with id= G, first strand: chain '2' and resid 628 through 630 Processing sheet with id= H, first strand: chain '3' and resid 95 through 97 removed outlier: 5.989A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain '3' and resid 273 through 279 removed outlier: 3.816A pdb=" N LYS 3 188 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN 3 259 " --> pdb=" O VAL 3 186 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 259 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 193 through 196 Processing sheet with id= K, first strand: chain '3' and resid 198 through 201 Processing sheet with id= L, first strand: chain '3' and resid 545 through 549 removed outlier: 6.358A pdb=" N VAL 3 512 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET 3 407 " --> pdb=" O VAL 3 512 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA 3 514 " --> pdb=" O MET 3 407 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA 3 516 " --> pdb=" O GLY 3 409 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 414 through 420 removed outlier: 3.545A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 339 through 342 Processing sheet with id= O, first strand: chain '4' and resid 344 through 348 removed outlier: 3.586A pdb=" N VAL 4 358 " --> pdb=" O ALA 4 345 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '4' and resid 604 through 606 Processing sheet with id= Q, first strand: chain '4' and resid 628 through 631 removed outlier: 6.408A pdb=" N SER 4 670 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE 4 631 " --> pdb=" O SER 4 670 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU 4 672 " --> pdb=" O ILE 4 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '4' and resid 654 through 658 Processing sheet with id= S, first strand: chain '5' and resid 60 through 64 removed outlier: 6.068A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain '5' and resid 291 through 297 removed outlier: 6.992A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU 5 274 " --> pdb=" O LEU 5 258 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR 5 275 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE 5 330 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '5' and resid 179 through 182 Processing sheet with id= V, first strand: chain '5' and resid 451 through 455 Processing sheet with id= W, first strand: chain '5' and resid 475 through 478 Processing sheet with id= X, first strand: chain '5' and resid 501 through 503 Processing sheet with id= Y, first strand: chain '5' and resid 173 through 178 removed outlier: 6.339A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '6' and resid 286 through 290 Processing sheet with id= AA, first strand: chain '6' and resid 359 through 362 Processing sheet with id= AB, first strand: chain '6' and resid 596 through 598 removed outlier: 3.628A pdb=" N CYS 6 637 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR 6 598 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain '7' and resid 238 through 241 Processing sheet with id= AD, first strand: chain '7' and resid 268 through 272 removed outlier: 3.547A pdb=" N VAL 7 269 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '7' and resid 330 through 336 removed outlier: 5.347A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain '7' and resid 456 through 458 removed outlier: 6.418A pdb=" N ILE 7 596 " --> pdb=" O CYS 7 457 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain '7' and resid 480 through 482 removed outlier: 6.651A pdb=" N ILE 7 520 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'B' and resid 68 through 72 Processing sheet with id= AI, first strand: chain 'C' and resid 42 through 47 removed outlier: 3.542A pdb=" N THR C 42 " --> pdb=" O PHE C 20 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 227 through 231 Processing sheet with id= AK, first strand: chain 'D' and resid 247 through 249 removed outlier: 3.533A pdb=" N LYS D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 260 " --> pdb=" O GLU D 265 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 265 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 57 through 61 removed outlier: 6.289A pdb=" N SER E 80 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE E 30 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU E 82 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER E 32 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL E 84 " --> pdb=" O SER E 32 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 316 through 324 removed outlier: 4.001A pdb=" N LEU E 413 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'E' and resid 525 through 530 removed outlier: 7.693A pdb=" N CYS E 528 " --> pdb=" O PRO E 566 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL E 568 " --> pdb=" O CYS E 528 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU E 530 " --> pdb=" O VAL E 568 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA E 570 " --> pdb=" O LEU E 530 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 526 through 530 removed outlier: 3.667A pdb=" N TYR F 526 " --> pdb=" O VAL F 515 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR F 511 " --> pdb=" O ASP F 530 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 505 " --> pdb=" O SER F 512 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER F 503 " --> pdb=" O THR F 514 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR F 495 " --> pdb=" O VAL F 502 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR F 504 " --> pdb=" O TYR F 493 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR F 493 " --> pdb=" O THR F 504 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS F 506 " --> pdb=" O ARG F 491 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG F 491 " --> pdb=" O LYS F 506 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 536 through 539 Processing sheet with id= AQ, first strand: chain 'F' and resid 580 through 583 Processing sheet with id= AR, first strand: chain 'F' and resid 635 through 642 removed outlier: 4.089A pdb=" N VAL F 628 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA F 617 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR F 630 " --> pdb=" O ILE F 615 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE F 615 " --> pdb=" O TYR F 630 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'F' and resid 686 through 689 Processing sheet with id= AT, first strand: chain 'F' and resid 705 through 708 Processing sheet with id= AU, first strand: chain 'F' and resid 740 through 743 removed outlier: 3.876A pdb=" N HIS F 741 " --> pdb=" O VAL F 757 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'F' and resid 751 through 754 Processing sheet with id= AW, first strand: chain 'G' and resid 511 through 517 removed outlier: 4.026A pdb=" N THR G 495 " --> pdb=" O VAL G 502 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR G 504 " --> pdb=" O TYR G 493 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TYR G 493 " --> pdb=" O THR G 504 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS G 506 " --> pdb=" O ARG G 491 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG G 491 " --> pdb=" O LYS G 506 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'G' and resid 536 through 540 Processing sheet with id= AY, first strand: chain 'G' and resid 580 through 583 removed outlier: 3.792A pdb=" N ARG G 598 " --> pdb=" O VAL G 590 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN G 601 " --> pdb=" O PRO G 606 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'G' and resid 617 through 620 removed outlier: 5.702A pdb=" N GLU G 642 " --> pdb=" O TYR G 650 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR G 650 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'G' and resid 696 through 698 Processing sheet with id= BB, first strand: chain 'G' and resid 771 through 775 removed outlier: 3.858A pdb=" N MET G 774 " --> pdb=" O LEU G 752 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE G 755 " --> pdb=" O PRO G 744 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL G 757 " --> pdb=" O VAL G 742 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL G 742 " --> pdb=" O VAL G 757 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'H' and resid 528 through 530 removed outlier: 3.534A pdb=" N TYR H 511 " --> pdb=" O ASP H 530 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N THR H 504 " --> pdb=" O TYR H 493 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR H 493 " --> pdb=" O THR H 504 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS H 506 " --> pdb=" O ARG H 491 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ARG H 491 " --> pdb=" O LYS H 506 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'H' and resid 536 through 540 Processing sheet with id= BE, first strand: chain 'H' and resid 580 through 583 removed outlier: 3.572A pdb=" N ARG H 598 " --> pdb=" O VAL H 590 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 608 " --> pdb=" O SER H 599 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'H' and resid 635 through 639 removed outlier: 3.681A pdb=" N VAL H 628 " --> pdb=" O ALA H 617 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA H 617 " --> pdb=" O VAL H 628 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR H 630 " --> pdb=" O ILE H 615 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE H 615 " --> pdb=" O TYR H 630 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'H' and resid 686 through 689 removed outlier: 4.242A pdb=" N LEU H 707 " --> pdb=" O PRO H 695 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'H' and resid 771 through 775 removed outlier: 3.545A pdb=" N ALA H 746 " --> pdb=" O ASN H 753 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE H 755 " --> pdb=" O PRO H 744 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL H 757 " --> pdb=" O VAL H 742 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL H 742 " --> pdb=" O VAL H 757 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'M' and resid 1325 through 1327 removed outlier: 3.586A pdb=" N GLN M1326 " --> pdb=" O GLU M1337 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'M' and resid 1725 through 1727 removed outlier: 3.782A pdb=" N TYR M1727 " --> pdb=" O LEU M1909 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU M1909 " --> pdb=" O TYR M1727 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'M' and resid 1729 through 1731 removed outlier: 4.238A pdb=" N ASN M1729 " --> pdb=" O THR M1870 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'N' and resid 171 through 173 removed outlier: 4.053A pdb=" N LYS N 171 " --> pdb=" O ALA N 533 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR N 638 " --> pdb=" O VAL N 540 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N PHE N 542 " --> pdb=" O THR N 638 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL N 640 " --> pdb=" O PHE N 542 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS N 657 " --> pdb=" O MET N 639 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU N 641 " --> pdb=" O LYS N 657 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE N 659 " --> pdb=" O LEU N 641 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'N' and resid 181 through 183 Processing sheet with id= BN, first strand: chain 'N' and resid 304 through 307 removed outlier: 4.191A pdb=" N TRP N 296 " --> pdb=" O ILE N 307 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE N 331 " --> pdb=" O VAL N 341 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL N 341 " --> pdb=" O ILE N 331 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'N' and resid 523 through 526 removed outlier: 6.201A pdb=" N MET N 481 " --> pdb=" O VAL N 524 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER N 526 " --> pdb=" O MET N 481 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE N 483 " --> pdb=" O SER N 526 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU N 432 " --> pdb=" O ILE N 482 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE N 484 " --> pdb=" O LEU N 432 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP N 434 " --> pdb=" O ILE N 484 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE N 401 " --> pdb=" O MET N 673 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS N 681 " --> pdb=" O VAL N 676 " (cutoff:3.500A) 2389 hydrogen bonds defined for protein. 6693 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: 24.04 Time building geometry restraints manager: 24.94 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: 20982 1.36 - 1.50: 16916 1.50 - 1.65: 26368 1.65 - 1.80: 280 1.80 - 1.95: 176 Bond restraints: 64722 Sorted by residual: bond pdb=" N PRO 5 525 " pdb=" CD PRO 5 525 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.14e+01 bond pdb=" C4 ADP 31001 " pdb=" C5 ADP 31001 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP 2 902 " pdb=" C5 ADP 2 902 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C GLY A 61 " pdb=" O GLY A 61 " ideal model delta sigma weight residual 1.235 1.306 -0.071 1.35e-02 5.49e+03 2.79e+01 bond pdb=" C LEU M1941 " pdb=" O LEU M1941 " ideal model delta sigma weight residual 1.236 1.303 -0.067 1.28e-02 6.10e+03 2.73e+01 ... (remaining 64717 not shown) Histogram of bond angle deviations from ideal: 97.11 - 104.77: 1096 104.77 - 112.43: 33991 112.43 - 120.10: 24161 120.10 - 127.76: 27914 127.76 - 135.43: 513 Bond angle restraints: 87675 Sorted by residual: angle pdb=" CA GLN A 57 " pdb=" C GLN A 57 " pdb=" O GLN A 57 " ideal model delta sigma weight residual 121.07 114.81 6.26 1.10e+00 8.26e-01 3.24e+01 angle pdb=" N ILE F 762 " pdb=" CA ILE F 762 " pdb=" C ILE F 762 " ideal model delta sigma weight residual 111.91 107.32 4.59 8.90e-01 1.26e+00 2.66e+01 angle pdb=" C GLU 6 116 " pdb=" N GLN 6 117 " pdb=" CA GLN 6 117 " ideal model delta sigma weight residual 120.72 112.13 8.59 1.67e+00 3.59e-01 2.64e+01 angle pdb=" C HIS 7 620 " pdb=" N MET 7 621 " pdb=" CA MET 7 621 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C GLN 7 291 " pdb=" N ASN 7 292 " pdb=" CA ASN 7 292 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 ... (remaining 87670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.30: 38266 32.30 - 64.59: 1055 64.59 - 96.89: 107 96.89 - 129.18: 2 129.18 - 161.48: 3 Dihedral angle restraints: 39433 sinusoidal: 16226 harmonic: 23207 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 300.00 138.53 161.48 1 2.00e+01 2.50e-03 4.68e+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 300.00 139.19 160.80 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP 2 902 " pdb=" O5' ADP 2 902 " pdb=" PA ADP 2 902 " pdb=" O2A ADP 2 902 " ideal model delta sinusoidal sigma weight residual -60.00 72.64 -132.64 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 39430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 8055 0.055 - 0.109: 1610 0.109 - 0.163: 291 0.163 - 0.218: 38 0.218 - 0.272: 6 Chirality restraints: 10000 Sorted by residual: chirality pdb=" CB ILE G 615 " pdb=" CA ILE G 615 " pdb=" CG1 ILE G 615 " pdb=" CG2 ILE G 615 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PHE M1944 " pdb=" N PHE M1944 " pdb=" C PHE M1944 " pdb=" CB PHE M1944 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE 6 715 " pdb=" CA ILE 6 715 " pdb=" CG1 ILE 6 715 " pdb=" CG2 ILE 6 715 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 9997 not shown) Planarity restraints: 11151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN M1940 " 0.024 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C GLN M1940 " -0.082 2.00e-02 2.50e+03 pdb=" O GLN M1940 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU M1941 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN 7 291 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C GLN 7 291 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN 7 291 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN 7 292 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 187 " 0.230 9.50e-02 1.11e+02 1.03e-01 6.53e+00 pdb=" NE ARG 6 187 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG 6 187 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 187 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 187 " 0.008 2.00e-02 2.50e+03 ... (remaining 11148 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 2 1.79 - 2.57: 1422 2.57 - 3.35: 97628 3.35 - 4.12: 180379 4.12 - 4.90: 304784 Nonbonded interactions: 584215 Sorted by model distance: nonbonded pdb=" ND2 ASN 3 312 " pdb=" O ASN 5 302 " model vdw 1.015 2.520 nonbonded pdb=" SD MET A 62 " pdb=" CB ALA A 68 " model vdw 1.699 3.820 nonbonded pdb=" OG SER 5 423 " pdb="MG MG 5 804 " model vdw 2.012 2.170 nonbonded pdb=" OH TYR 3 38 " pdb=" OD2 ASP 3 102 " model vdw 2.036 2.440 nonbonded pdb=" OG SER D 176 " pdb=" OD1 ASP D 178 " model vdw 2.049 2.440 ... (remaining 584210 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 663 or resid 670 through 789 or (resid 790 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 892 o \ r (resid 893 through 894 and (name N or name CA or name C or name O or name CB ) \ ) or resid 895 through 901 or (resid 902 and (name N or name CA or name C or nam \ e O or name CB )) or resid 903 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 923)) selection = (chain 'G' and (resid 474 through 789 or (resid 790 and (name N or name CA or na \ me C or name O or name CB )) or resid 814 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 (name N or name CA or name C or name O or name CB )) or resid 911 throug \ h 923)) selection = (chain 'H' and (resid 474 through 663 or resid 670 through 892 or (resid 893 thr \ ough 894 and (name N or name CA or name C or name O or name CB )) or resid 895 t \ hrough 909 or (resid 910 and (name N or name CA or name C or name O or name CB ) \ ) or resid 911 or (resid 912 and (name N or name CA or name C or name O or name \ CB )) or resid 913 through 923)) } 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: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 18.240 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 145.740 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 64722 Z= 0.261 Angle : 0.772 14.925 87675 Z= 0.435 Chirality : 0.046 0.272 10000 Planarity : 0.005 0.103 11151 Dihedral : 14.795 161.476 24353 Min Nonbonded Distance : 1.015 Molprobity Statistics. All-atom Clashscore : 36.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.96 % Favored : 93.79 % Rotamer: Outliers : 0.74 % Allowed : 0.69 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.09), residues: 7772 helix: 0.97 (0.09), residues: 3100 sheet: -0.66 (0.15), residues: 1142 loop : -1.04 (0.10), residues: 3530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 624 HIS 0.008 0.001 HIS 6 653 PHE 0.043 0.002 PHE 6 142 TYR 0.034 0.002 TYR 4 519 ARG 0.015 0.001 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 180 time to evaluate : 5.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9106 (ptp) cc_final: 0.8895 (ptp) REVERT: 2 783 MET cc_start: 0.9557 (mpp) cc_final: 0.8998 (tpt) REVERT: 2 788 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8864 (ptp-110) REVERT: 3 384 MET cc_start: 0.9077 (tpp) cc_final: 0.8828 (tpt) REVERT: 4 801 MET cc_start: 0.7158 (mmp) cc_final: 0.6829 (mmm) REVERT: 5 276 MET cc_start: 0.9402 (mpp) cc_final: 0.8818 (mpp) REVERT: 5 393 MET cc_start: 0.8108 (tpt) cc_final: 0.7518 (tpt) REVERT: 5 404 MET cc_start: 0.8608 (mmt) cc_final: 0.8080 (mmm) REVERT: 6 551 MET cc_start: 0.9417 (mmp) cc_final: 0.9148 (mmm) REVERT: 6 706 MET cc_start: 0.9077 (ppp) cc_final: 0.8856 (ppp) REVERT: 7 541 MET cc_start: 0.9554 (ppp) cc_final: 0.9243 (ppp) REVERT: A 58 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.6104 (tm-30) REVERT: A 75 THR cc_start: 0.9863 (OUTLIER) cc_final: 0.9622 (p) REVERT: A 79 MET cc_start: 0.9814 (ptp) cc_final: 0.9578 (ptp) REVERT: A 100 MET cc_start: 0.9718 (mmp) cc_final: 0.9511 (mmm) REVERT: B 189 MET cc_start: 0.9111 (tpt) cc_final: 0.8058 (tpt) REVERT: C 79 MET cc_start: 0.9240 (tpt) cc_final: 0.8996 (tpp) REVERT: D 129 MET cc_start: 0.9392 (mtt) cc_final: 0.9019 (tpp) REVERT: E 44 MET cc_start: 0.9465 (mmt) cc_final: 0.9236 (mmm) REVERT: F 726 MET cc_start: 0.9523 (tpt) cc_final: 0.9212 (tpt) REVERT: F 774 MET cc_start: 0.9547 (mmp) cc_final: 0.9343 (mmm) REVERT: F 821 MET cc_start: 0.9322 (tpt) cc_final: 0.8878 (tpt) REVERT: G 778 MET cc_start: 0.8218 (mpp) cc_final: 0.6942 (pmm) REVERT: H 496 MET cc_start: 0.9522 (mpp) cc_final: 0.9298 (mpp) REVERT: H 659 MET cc_start: 0.7226 (ppp) cc_final: 0.7015 (ppp) REVERT: M 1894 MET cc_start: 0.8550 (pmm) cc_final: 0.7901 (ppp) REVERT: M 2012 MET cc_start: 0.7731 (ppp) cc_final: 0.7159 (ppp) outliers start: 52 outliers final: 20 residues processed: 229 average time/residue: 0.6043 time to fit residues: 242.2787 Evaluate side-chains 200 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 5.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 662 optimal weight: 50.0000 chunk 594 optimal weight: 1.9990 chunk 329 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 400 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 614 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 373 optimal weight: 20.0000 chunk 457 optimal weight: 9.9990 chunk 711 optimal weight: 30.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN ** 5 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 334 GLN 5 499 GLN ** 5 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 182 GLN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS ** 6 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 518 ASN ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1950 GLN ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 64722 Z= 0.244 Angle : 0.651 11.372 87675 Z= 0.345 Chirality : 0.043 0.254 10000 Planarity : 0.005 0.084 11151 Dihedral : 8.606 155.121 8872 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 36.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.94 % Favored : 93.93 % Rotamer: Outliers : 0.11 % Allowed : 6.90 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.09), residues: 7772 helix: 0.87 (0.09), residues: 3162 sheet: -0.78 (0.15), residues: 1147 loop : -1.09 (0.10), residues: 3463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 624 HIS 0.018 0.001 HIS 6 730 PHE 0.029 0.002 PHE A 73 TYR 0.037 0.002 TYR 6 754 ARG 0.011 0.001 ARG 2 836 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 5.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.9584 (mpp) cc_final: 0.9074 (tpp) REVERT: 3 136 MET cc_start: 0.8463 (tmm) cc_final: 0.8239 (tmm) REVERT: 3 384 MET cc_start: 0.9051 (tpp) cc_final: 0.8792 (tpt) REVERT: 4 199 MET cc_start: 0.9490 (pmm) cc_final: 0.9241 (pmm) REVERT: 4 801 MET cc_start: 0.6944 (mmp) cc_final: 0.6613 (mmm) REVERT: 5 393 MET cc_start: 0.8286 (tpt) cc_final: 0.7796 (tpt) REVERT: 5 404 MET cc_start: 0.8626 (mmt) cc_final: 0.8155 (mmm) REVERT: 6 551 MET cc_start: 0.9504 (mmp) cc_final: 0.9254 (mmm) REVERT: 6 644 MET cc_start: 0.7931 (mmt) cc_final: 0.7503 (mmt) REVERT: 6 706 MET cc_start: 0.9125 (ppp) cc_final: 0.8855 (ppp) REVERT: 7 541 MET cc_start: 0.9553 (ppp) cc_final: 0.9290 (ppp) REVERT: B 189 MET cc_start: 0.9173 (tpt) cc_final: 0.8020 (tpt) REVERT: C 79 MET cc_start: 0.9303 (tpt) cc_final: 0.8989 (tpp) REVERT: D 129 MET cc_start: 0.9538 (mtt) cc_final: 0.9185 (tpp) REVERT: E 44 MET cc_start: 0.9467 (mmt) cc_final: 0.9206 (mmt) REVERT: F 659 MET cc_start: 0.8761 (tmm) cc_final: 0.8485 (tmm) REVERT: F 726 MET cc_start: 0.9556 (tpt) cc_final: 0.9195 (tpt) REVERT: F 821 MET cc_start: 0.9355 (tpt) cc_final: 0.8883 (tpp) REVERT: G 778 MET cc_start: 0.8267 (mpp) cc_final: 0.7029 (pmm) REVERT: M 1894 MET cc_start: 0.8697 (pmm) cc_final: 0.8012 (ppp) REVERT: M 1957 MET cc_start: 0.8656 (ppp) cc_final: 0.8332 (ppp) outliers start: 8 outliers final: 4 residues processed: 190 average time/residue: 0.5497 time to fit residues: 188.9379 Evaluate side-chains 182 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 5.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 395 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 592 optimal weight: 40.0000 chunk 484 optimal weight: 30.0000 chunk 196 optimal weight: 7.9990 chunk 713 optimal weight: 30.0000 chunk 770 optimal weight: 0.0770 chunk 635 optimal weight: 9.9990 chunk 707 optimal weight: 40.0000 chunk 243 optimal weight: 0.8980 chunk 572 optimal weight: 30.0000 overall best weight: 3.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 248 HIS ** 2 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN 5 344 ASN 5 499 GLN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 ASN A 90 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 340 HIS ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 64722 Z= 0.201 Angle : 0.631 11.605 87675 Z= 0.330 Chirality : 0.043 0.217 10000 Planarity : 0.005 0.066 11151 Dihedral : 8.484 159.762 8872 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 32.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.84 % Favored : 94.03 % Rotamer: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.95 % 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: -0.36 (0.09), residues: 7772 helix: 0.90 (0.09), residues: 3154 sheet: -0.82 (0.15), residues: 1146 loop : -1.05 (0.10), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M1956 HIS 0.014 0.001 HIS 6 730 PHE 0.035 0.002 PHE 7 355 TYR 0.029 0.002 TYR 6 754 ARG 0.013 0.001 ARG F 868 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 5.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.9590 (mpp) cc_final: 0.9065 (tpp) REVERT: 3 136 MET cc_start: 0.8583 (tmm) cc_final: 0.8288 (tmm) REVERT: 3 384 MET cc_start: 0.8999 (tpp) cc_final: 0.8785 (tpt) REVERT: 3 407 MET cc_start: 0.9648 (tmm) cc_final: 0.9447 (tmm) REVERT: 4 801 MET cc_start: 0.7014 (mmp) cc_final: 0.6700 (mmm) REVERT: 5 276 MET cc_start: 0.9084 (mpp) cc_final: 0.8878 (mpp) REVERT: 5 404 MET cc_start: 0.8502 (mmt) cc_final: 0.8046 (mmm) REVERT: 5 469 MET cc_start: 0.9772 (mpp) cc_final: 0.9241 (mmp) REVERT: 6 551 MET cc_start: 0.9544 (mmp) cc_final: 0.9311 (mmm) REVERT: 6 644 MET cc_start: 0.7755 (mmt) cc_final: 0.7238 (mmt) REVERT: 7 541 MET cc_start: 0.9568 (ppp) cc_final: 0.9301 (ppp) REVERT: B 189 MET cc_start: 0.9098 (tpt) cc_final: 0.7942 (tpt) REVERT: C 79 MET cc_start: 0.9317 (tpt) cc_final: 0.8964 (tpp) REVERT: D 129 MET cc_start: 0.9548 (mtt) cc_final: 0.9219 (tpp) REVERT: E 44 MET cc_start: 0.9431 (mmt) cc_final: 0.9162 (mmm) REVERT: F 659 MET cc_start: 0.8789 (tmm) cc_final: 0.8476 (tmm) REVERT: F 726 MET cc_start: 0.9582 (tpt) cc_final: 0.9209 (tpp) REVERT: F 821 MET cc_start: 0.9363 (tpt) cc_final: 0.8840 (tpt) REVERT: G 778 MET cc_start: 0.8226 (mpp) cc_final: 0.6948 (pmm) REVERT: M 1894 MET cc_start: 0.8784 (pmm) cc_final: 0.8081 (ppp) REVERT: M 1957 MET cc_start: 0.8658 (ppp) cc_final: 0.8324 (ppp) outliers start: 6 outliers final: 5 residues processed: 187 average time/residue: 0.5849 time to fit residues: 198.0787 Evaluate side-chains 183 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 6.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 704 optimal weight: 20.0000 chunk 536 optimal weight: 20.0000 chunk 370 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 340 optimal weight: 40.0000 chunk 478 optimal weight: 20.0000 chunk 715 optimal weight: 30.0000 chunk 757 optimal weight: 0.0050 chunk 373 optimal weight: 10.0000 chunk 678 optimal weight: 50.0000 chunk 204 optimal weight: 30.0000 overall best weight: 14.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 683 ASN 4 691 ASN ** 4 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 895 GLN ** 5 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 209 GLN ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 554 ASN ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** E 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1892 ASN ** M1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1950 GLN M1975 ASN ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 216 GLN ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.164 64722 Z= 0.461 Angle : 0.853 12.380 87675 Z= 0.453 Chirality : 0.047 0.235 10000 Planarity : 0.006 0.085 11151 Dihedral : 8.900 159.437 8872 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 57.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.12 % Favored : 92.69 % Rotamer: Outliers : 0.19 % Allowed : 7.25 % Favored : 92.56 % 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: -1.17 (0.09), residues: 7772 helix: 0.07 (0.09), residues: 3143 sheet: -1.24 (0.15), residues: 1099 loop : -1.33 (0.10), residues: 3530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 743 HIS 0.017 0.002 HIS B 108 PHE 0.033 0.003 PHE F 626 TYR 0.029 0.003 TYR 7 618 ARG 0.017 0.001 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 5.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9257 (ptp) cc_final: 0.8923 (ptp) REVERT: 3 136 MET cc_start: 0.8403 (tmm) cc_final: 0.8063 (tmm) REVERT: 3 386 MET cc_start: 0.9210 (tpt) cc_final: 0.8959 (tpp) REVERT: 3 407 MET cc_start: 0.9578 (tmm) cc_final: 0.9303 (tmm) REVERT: 5 276 MET cc_start: 0.9139 (mpp) cc_final: 0.8781 (mpp) REVERT: 5 404 MET cc_start: 0.8916 (mmt) cc_final: 0.8477 (mmm) REVERT: 6 644 MET cc_start: 0.8001 (mmt) cc_final: 0.7571 (mmt) REVERT: 7 506 MET cc_start: 0.4994 (mmp) cc_final: 0.4697 (mmp) REVERT: 7 529 MET cc_start: 0.8480 (ppp) cc_final: 0.7763 (ppp) REVERT: 7 541 MET cc_start: 0.9594 (ppp) cc_final: 0.9369 (ppp) REVERT: B 189 MET cc_start: 0.9297 (tpt) cc_final: 0.8261 (tpt) REVERT: C 79 MET cc_start: 0.9449 (tpt) cc_final: 0.8922 (tpp) REVERT: D 129 MET cc_start: 0.9653 (mtt) cc_final: 0.9427 (mtt) REVERT: E 44 MET cc_start: 0.9575 (mmt) cc_final: 0.9248 (mmt) REVERT: F 726 MET cc_start: 0.9612 (tpt) cc_final: 0.9198 (tpt) REVERT: F 821 MET cc_start: 0.9335 (tpt) cc_final: 0.8820 (tpt) REVERT: H 752 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9404 (tt) REVERT: M 1957 MET cc_start: 0.8781 (ppp) cc_final: 0.8459 (ppp) outliers start: 13 outliers final: 3 residues processed: 191 average time/residue: 0.5642 time to fit residues: 195.4819 Evaluate side-chains 181 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 5.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 631 optimal weight: 7.9990 chunk 430 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 564 optimal weight: 6.9990 chunk 312 optimal weight: 20.0000 chunk 646 optimal weight: 10.0000 chunk 523 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 386 optimal weight: 7.9990 chunk 680 optimal weight: 8.9990 chunk 191 optimal weight: 30.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 549 ASN 4 576 GLN 4 691 ASN ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 24 ASN ** 5 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 359 GLN 5 499 GLN ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 514 ASN ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 915 ASN ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 216 GLN ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 64722 Z= 0.295 Angle : 0.712 12.151 87675 Z= 0.376 Chirality : 0.044 0.280 10000 Planarity : 0.005 0.082 11151 Dihedral : 8.796 161.608 8872 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 44.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.47 % Favored : 93.36 % Rotamer: Outliers : 0.01 % Allowed : 4.08 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.09), residues: 7772 helix: 0.30 (0.09), residues: 3145 sheet: -1.16 (0.15), residues: 1066 loop : -1.33 (0.10), residues: 3561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP M1956 HIS 0.012 0.002 HIS H 629 PHE 0.027 0.002 PHE M1915 TYR 0.030 0.002 TYR 6 828 ARG 0.015 0.001 ARG 2 836 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 5.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9118 (ptp) cc_final: 0.8732 (ptp) REVERT: 3 384 MET cc_start: 0.9012 (tpp) cc_final: 0.8783 (tpt) REVERT: 3 386 MET cc_start: 0.9240 (tpt) cc_final: 0.8998 (tpp) REVERT: 4 199 MET cc_start: 0.9565 (pmm) cc_final: 0.9320 (pmm) REVERT: 4 801 MET cc_start: 0.7147 (mmp) cc_final: 0.6927 (mmm) REVERT: 5 276 MET cc_start: 0.9211 (mpp) cc_final: 0.9005 (mpp) REVERT: 5 404 MET cc_start: 0.8689 (mmt) cc_final: 0.8245 (mmm) REVERT: 5 599 MET cc_start: 0.9880 (mmt) cc_final: 0.9639 (mmm) REVERT: 6 644 MET cc_start: 0.7952 (mmt) cc_final: 0.7546 (mmt) REVERT: 6 706 MET cc_start: 0.9258 (ppp) cc_final: 0.9006 (ppp) REVERT: 7 506 MET cc_start: 0.4752 (mmp) cc_final: 0.4464 (mmp) REVERT: 7 529 MET cc_start: 0.8556 (ppp) cc_final: 0.7867 (ppp) REVERT: 7 541 MET cc_start: 0.9608 (ppp) cc_final: 0.9372 (ppp) REVERT: B 189 MET cc_start: 0.9160 (tpt) cc_final: 0.7979 (tpt) REVERT: C 79 MET cc_start: 0.9310 (tpt) cc_final: 0.8878 (tpp) REVERT: D 129 MET cc_start: 0.9654 (mtt) cc_final: 0.9432 (mtt) REVERT: E 44 MET cc_start: 0.9485 (mmt) cc_final: 0.9199 (mmm) REVERT: F 659 MET cc_start: 0.8744 (tmm) cc_final: 0.8516 (tmm) REVERT: F 726 MET cc_start: 0.9589 (tpt) cc_final: 0.9166 (tpt) REVERT: F 778 MET cc_start: 0.9587 (mpp) cc_final: 0.9375 (mpp) REVERT: F 821 MET cc_start: 0.9397 (tpt) cc_final: 0.8859 (tpt) REVERT: G 778 MET cc_start: 0.8117 (mpp) cc_final: 0.6930 (pmm) REVERT: G 847 MET cc_start: 0.8154 (ptt) cc_final: 0.7932 (pmm) REVERT: M 1957 MET cc_start: 0.8538 (ppp) cc_final: 0.8213 (ppp) REVERT: M 2062 MET cc_start: 0.9034 (mtm) cc_final: 0.8803 (mtp) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.5593 time to fit residues: 181.1014 Evaluate side-chains 177 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 5.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 254 optimal weight: 7.9990 chunk 682 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 444 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 758 optimal weight: 30.0000 chunk 629 optimal weight: 0.0060 chunk 351 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 398 optimal weight: 20.0000 overall best weight: 5.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 641 GLN ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 499 GLN 5 514 ASN 5 574 ASN 5 581 ASN ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 916 ASN ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1534 GLN ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 ASN ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 64722 Z= 0.229 Angle : 0.670 14.561 87675 Z= 0.351 Chirality : 0.044 0.221 10000 Planarity : 0.005 0.078 11151 Dihedral : 8.680 161.501 8872 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 38.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.50 % Favored : 93.32 % Rotamer: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.80 (0.09), residues: 7772 helix: 0.53 (0.09), residues: 3155 sheet: -1.12 (0.15), residues: 1096 loop : -1.27 (0.10), residues: 3521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M1956 HIS 0.010 0.001 HIS 6 730 PHE 0.021 0.002 PHE M1558 TYR 0.042 0.002 TYR 4 226 ARG 0.017 0.001 ARG G 649 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 182 time to evaluate : 5.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9129 (ptp) cc_final: 0.8775 (ptp) REVERT: 3 306 MET cc_start: 0.9348 (tmm) cc_final: 0.8977 (mmp) REVERT: 3 384 MET cc_start: 0.8964 (tpp) cc_final: 0.8684 (tpt) REVERT: 3 407 MET cc_start: 0.9566 (tmm) cc_final: 0.9319 (tmm) REVERT: 4 199 MET cc_start: 0.9596 (pmm) cc_final: 0.9348 (pmm) REVERT: 5 404 MET cc_start: 0.8455 (mmt) cc_final: 0.8024 (mmm) REVERT: 5 599 MET cc_start: 0.9869 (mmt) cc_final: 0.9585 (mmm) REVERT: 6 644 MET cc_start: 0.7983 (mmt) cc_final: 0.7565 (mmt) REVERT: 6 706 MET cc_start: 0.9243 (ppp) cc_final: 0.8972 (ppp) REVERT: 7 64 MET cc_start: 0.9715 (mpp) cc_final: 0.9493 (mpp) REVERT: 7 506 MET cc_start: 0.4830 (mmp) cc_final: 0.4582 (mmp) REVERT: 7 541 MET cc_start: 0.9609 (ppp) cc_final: 0.9375 (ppp) REVERT: B 66 MET cc_start: 0.8843 (tpt) cc_final: 0.8537 (tpp) REVERT: B 189 MET cc_start: 0.9115 (tpt) cc_final: 0.7797 (tpt) REVERT: C 79 MET cc_start: 0.9236 (tpt) cc_final: 0.8836 (tpp) REVERT: E 44 MET cc_start: 0.9444 (mmt) cc_final: 0.9114 (mmm) REVERT: E 567 MET cc_start: 0.9406 (mmp) cc_final: 0.8422 (mpp) REVERT: F 659 MET cc_start: 0.8547 (tmm) cc_final: 0.8326 (tmm) REVERT: F 726 MET cc_start: 0.9530 (tpt) cc_final: 0.9088 (tpp) REVERT: F 821 MET cc_start: 0.9397 (tpt) cc_final: 0.8871 (tpt) REVERT: G 778 MET cc_start: 0.8046 (mpp) cc_final: 0.6822 (pmm) REVERT: M 1957 MET cc_start: 0.8513 (ppp) cc_final: 0.8200 (ppp) REVERT: M 2062 MET cc_start: 0.9010 (mtm) cc_final: 0.8796 (mtp) outliers start: 4 outliers final: 2 residues processed: 186 average time/residue: 0.5761 time to fit residues: 193.3493 Evaluate side-chains 182 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 5.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 731 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 432 optimal weight: 4.9990 chunk 553 optimal weight: 5.9990 chunk 429 optimal weight: 7.9990 chunk 638 optimal weight: 8.9990 chunk 423 optimal weight: 2.9990 chunk 755 optimal weight: 30.0000 chunk 472 optimal weight: 9.9990 chunk 460 optimal weight: 8.9990 chunk 348 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 192 ASN ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 499 GLN 5 581 ASN ** 5 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 ASN ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 64722 Z= 0.225 Angle : 0.671 13.608 87675 Z= 0.350 Chirality : 0.044 0.307 10000 Planarity : 0.005 0.070 11151 Dihedral : 8.616 161.719 8872 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 37.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.09), residues: 7772 helix: 0.59 (0.09), residues: 3146 sheet: -1.08 (0.15), residues: 1079 loop : -1.20 (0.10), residues: 3547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M1956 HIS 0.006 0.001 HIS H 629 PHE 0.025 0.002 PHE 6 115 TYR 0.034 0.002 TYR 4 226 ARG 0.017 0.001 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 5.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9121 (ptp) cc_final: 0.8790 (ptp) REVERT: 3 306 MET cc_start: 0.9385 (tmm) cc_final: 0.8926 (mmp) REVERT: 3 386 MET cc_start: 0.9272 (tpt) cc_final: 0.8986 (tpp) REVERT: 4 199 MET cc_start: 0.9595 (pmm) cc_final: 0.9355 (pmm) REVERT: 4 637 MET cc_start: 0.5044 (mmp) cc_final: 0.4710 (mmt) REVERT: 5 276 MET cc_start: 0.9204 (mpp) cc_final: 0.8747 (mpp) REVERT: 5 404 MET cc_start: 0.8562 (mmt) cc_final: 0.8175 (mmm) REVERT: 5 599 MET cc_start: 0.9868 (mmt) cc_final: 0.9587 (mmm) REVERT: 6 644 MET cc_start: 0.7925 (mmt) cc_final: 0.7419 (mmt) REVERT: 6 706 MET cc_start: 0.9257 (ppp) cc_final: 0.8992 (ppp) REVERT: 7 506 MET cc_start: 0.4886 (mmp) cc_final: 0.4632 (mmp) REVERT: 7 529 MET cc_start: 0.8447 (ppp) cc_final: 0.7845 (ppp) REVERT: 7 541 MET cc_start: 0.9606 (ppp) cc_final: 0.9369 (ppp) REVERT: B 189 MET cc_start: 0.9091 (tpt) cc_final: 0.7735 (tpt) REVERT: C 79 MET cc_start: 0.9208 (tpt) cc_final: 0.8844 (tpp) REVERT: D 129 MET cc_start: 0.9692 (mtp) cc_final: 0.9366 (mtt) REVERT: E 44 MET cc_start: 0.9456 (mmt) cc_final: 0.9107 (mmm) REVERT: E 567 MET cc_start: 0.9430 (mmp) cc_final: 0.8465 (mpp) REVERT: F 659 MET cc_start: 0.8585 (tmm) cc_final: 0.8325 (tmm) REVERT: F 726 MET cc_start: 0.9511 (tpt) cc_final: 0.9037 (tpp) REVERT: F 821 MET cc_start: 0.9343 (tpt) cc_final: 0.8725 (tpt) REVERT: G 778 MET cc_start: 0.8014 (mpp) cc_final: 0.6809 (pmm) REVERT: M 1957 MET cc_start: 0.8556 (ppp) cc_final: 0.8265 (ppp) REVERT: M 2062 MET cc_start: 0.9013 (mtm) cc_final: 0.8803 (mtp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.5900 time to fit residues: 192.3408 Evaluate side-chains 180 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 5.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 467 optimal weight: 0.8980 chunk 301 optimal weight: 9.9990 chunk 451 optimal weight: 0.0770 chunk 227 optimal weight: 30.0000 chunk 148 optimal weight: 40.0000 chunk 146 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 chunk 514 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 chunk 593 optimal weight: 20.0000 overall best weight: 2.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 492 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN ** 4 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 893 HIS 5 581 ASN ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 568 ASN ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 629 HIS ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 64722 Z= 0.185 Angle : 0.658 12.968 87675 Z= 0.340 Chirality : 0.044 0.248 10000 Planarity : 0.004 0.064 11151 Dihedral : 8.500 162.472 8872 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 31.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.19 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: -0.56 (0.09), residues: 7772 helix: 0.73 (0.09), residues: 3160 sheet: -0.97 (0.15), residues: 1086 loop : -1.15 (0.10), residues: 3526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M1956 HIS 0.007 0.001 HIS 3 487 PHE 0.023 0.002 PHE N 207 TYR 0.028 0.002 TYR 4 226 ARG 0.018 0.001 ARG 6 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 5.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9109 (ptp) cc_final: 0.8881 (ptp) REVERT: 3 306 MET cc_start: 0.9346 (tmm) cc_final: 0.8905 (mmp) REVERT: 3 384 MET cc_start: 0.9084 (tpp) cc_final: 0.8724 (tpt) REVERT: 3 386 MET cc_start: 0.9215 (tpt) cc_final: 0.8945 (tpp) REVERT: 4 637 MET cc_start: 0.4648 (mmp) cc_final: 0.4345 (mmt) REVERT: 5 276 MET cc_start: 0.9182 (mpp) cc_final: 0.8829 (mpp) REVERT: 5 404 MET cc_start: 0.8265 (mmt) cc_final: 0.7920 (mmm) REVERT: 6 644 MET cc_start: 0.8021 (mmt) cc_final: 0.7573 (mmt) REVERT: 6 706 MET cc_start: 0.9254 (ppp) cc_final: 0.9013 (ppp) REVERT: 7 506 MET cc_start: 0.4825 (mmp) cc_final: 0.4576 (mmp) REVERT: 7 529 MET cc_start: 0.8513 (ppp) cc_final: 0.7897 (ppp) REVERT: 7 541 MET cc_start: 0.9598 (ppp) cc_final: 0.9356 (ppp) REVERT: B 189 MET cc_start: 0.9065 (tpt) cc_final: 0.7669 (tpt) REVERT: C 79 MET cc_start: 0.9171 (tpt) cc_final: 0.8799 (tpp) REVERT: D 129 MET cc_start: 0.9677 (mtp) cc_final: 0.9378 (mtt) REVERT: E 44 MET cc_start: 0.9419 (mmt) cc_final: 0.9082 (mmm) REVERT: E 567 MET cc_start: 0.9409 (mmp) cc_final: 0.8432 (mpp) REVERT: F 659 MET cc_start: 0.8577 (tmm) cc_final: 0.8297 (tmm) REVERT: F 726 MET cc_start: 0.9498 (tpt) cc_final: 0.9038 (tpp) REVERT: F 774 MET cc_start: 0.9646 (mmp) cc_final: 0.9396 (mmm) REVERT: F 821 MET cc_start: 0.9363 (tpt) cc_final: 0.8776 (tpt) REVERT: G 778 MET cc_start: 0.8136 (mpp) cc_final: 0.6945 (pmm) REVERT: M 1957 MET cc_start: 0.8464 (ppp) cc_final: 0.8184 (ppp) REVERT: M 2062 MET cc_start: 0.9046 (mtm) cc_final: 0.8821 (mtp) REVERT: N 91 MET cc_start: 0.8798 (mpp) cc_final: 0.8581 (mpp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.5795 time to fit residues: 190.5759 Evaluate side-chains 180 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 5.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 687 optimal weight: 40.0000 chunk 723 optimal weight: 6.9990 chunk 660 optimal weight: 8.9990 chunk 704 optimal weight: 0.0060 chunk 423 optimal weight: 5.9990 chunk 306 optimal weight: 30.0000 chunk 552 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 636 optimal weight: 4.9990 chunk 665 optimal weight: 50.0000 chunk 701 optimal weight: 5.9990 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN 5 581 ASN ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 833 GLN ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 64722 Z= 0.217 Angle : 0.657 12.881 87675 Z= 0.344 Chirality : 0.043 0.217 10000 Planarity : 0.005 0.063 11151 Dihedral : 8.487 160.910 8872 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 34.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.34 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.09), residues: 7772 helix: 0.74 (0.09), residues: 3142 sheet: -0.97 (0.15), residues: 1062 loop : -1.14 (0.10), residues: 3568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M1956 HIS 0.007 0.001 HIS 3 487 PHE 0.031 0.002 PHE 6 115 TYR 0.026 0.002 TYR 4 226 ARG 0.017 0.001 ARG H 868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 5.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9105 (ptp) cc_final: 0.8787 (ptp) REVERT: 3 306 MET cc_start: 0.9350 (tmm) cc_final: 0.9067 (mmp) REVERT: 3 384 MET cc_start: 0.9060 (tpp) cc_final: 0.8722 (tpt) REVERT: 3 386 MET cc_start: 0.9235 (tpt) cc_final: 0.8945 (tpp) REVERT: 4 637 MET cc_start: 0.4614 (mmp) cc_final: 0.4343 (mmt) REVERT: 5 404 MET cc_start: 0.8480 (mmt) cc_final: 0.8096 (mmm) REVERT: 5 599 MET cc_start: 0.9704 (mmp) cc_final: 0.9451 (mmm) REVERT: 6 644 MET cc_start: 0.7983 (mmt) cc_final: 0.7460 (mmt) REVERT: 6 706 MET cc_start: 0.9268 (ppp) cc_final: 0.9006 (ppp) REVERT: 7 506 MET cc_start: 0.4998 (mmp) cc_final: 0.4746 (mmp) REVERT: 7 529 MET cc_start: 0.8566 (ppp) cc_final: 0.8034 (ppp) REVERT: 7 541 MET cc_start: 0.9606 (ppp) cc_final: 0.9376 (ppp) REVERT: B 189 MET cc_start: 0.9113 (tpt) cc_final: 0.7889 (tpt) REVERT: C 79 MET cc_start: 0.9175 (tpt) cc_final: 0.8808 (tpp) REVERT: D 129 MET cc_start: 0.9688 (mtp) cc_final: 0.9372 (mtt) REVERT: E 44 MET cc_start: 0.9457 (mmt) cc_final: 0.9100 (mmm) REVERT: F 659 MET cc_start: 0.8569 (tmm) cc_final: 0.8276 (tmm) REVERT: F 726 MET cc_start: 0.9516 (tpt) cc_final: 0.9084 (tpp) REVERT: F 774 MET cc_start: 0.9652 (mmp) cc_final: 0.9404 (mmm) REVERT: F 821 MET cc_start: 0.9368 (tpt) cc_final: 0.8803 (tpt) REVERT: G 778 MET cc_start: 0.8073 (mpp) cc_final: 0.6847 (pmm) REVERT: M 1957 MET cc_start: 0.8416 (ppp) cc_final: 0.8147 (ppp) REVERT: M 2062 MET cc_start: 0.9105 (mtm) cc_final: 0.8871 (mtp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.5983 time to fit residues: 195.2567 Evaluate side-chains 179 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 5.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 462 optimal weight: 7.9990 chunk 744 optimal weight: 50.0000 chunk 454 optimal weight: 4.9990 chunk 353 optimal weight: 20.0000 chunk 517 optimal weight: 0.6980 chunk 781 optimal weight: 10.0000 chunk 718 optimal weight: 0.1980 chunk 621 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 480 optimal weight: 6.9990 chunk 381 optimal weight: 0.1980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 192 ASN ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN 5 581 ASN ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 833 GLN ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 64722 Z= 0.185 Angle : 0.653 12.361 87675 Z= 0.339 Chirality : 0.043 0.216 10000 Planarity : 0.004 0.059 11151 Dihedral : 8.416 160.822 8872 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 30.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.19 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.10), residues: 7772 helix: 0.77 (0.09), residues: 3146 sheet: -0.91 (0.15), residues: 1093 loop : -1.09 (0.11), residues: 3533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M1956 HIS 0.010 0.001 HIS 3 487 PHE 0.025 0.001 PHE 6 115 TYR 0.031 0.002 TYR 6 828 ARG 0.013 0.001 ARG H 868 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15544 Ramachandran restraints generated. 7772 Oldfield, 0 Emsley, 7772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 5.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9080 (ptp) cc_final: 0.8753 (ptp) REVERT: 2 276 MET cc_start: 0.9638 (mmp) cc_final: 0.9437 (mmm) REVERT: 3 384 MET cc_start: 0.9052 (tpp) cc_final: 0.8714 (tpt) REVERT: 3 386 MET cc_start: 0.9259 (tpt) cc_final: 0.8918 (tpp) REVERT: 4 637 MET cc_start: 0.4545 (mmp) cc_final: 0.4330 (mmt) REVERT: 5 276 MET cc_start: 0.9225 (mpp) cc_final: 0.8827 (mpp) REVERT: 5 404 MET cc_start: 0.8359 (mmt) cc_final: 0.7986 (mmm) REVERT: 6 644 MET cc_start: 0.7957 (mmt) cc_final: 0.7507 (mmt) REVERT: 6 706 MET cc_start: 0.9274 (ppp) cc_final: 0.9030 (ppp) REVERT: 7 506 MET cc_start: 0.4959 (mmp) cc_final: 0.4702 (mmp) REVERT: 7 529 MET cc_start: 0.8581 (ppp) cc_final: 0.8003 (ppp) REVERT: 7 541 MET cc_start: 0.9600 (ppp) cc_final: 0.9265 (ppp) REVERT: B 189 MET cc_start: 0.9063 (tpt) cc_final: 0.7789 (tpt) REVERT: C 79 MET cc_start: 0.9120 (tpt) cc_final: 0.8744 (tpp) REVERT: D 129 MET cc_start: 0.9697 (mtp) cc_final: 0.9409 (mtt) REVERT: E 1 MET cc_start: 0.8718 (mmt) cc_final: 0.8437 (mmt) REVERT: E 44 MET cc_start: 0.9415 (mmt) cc_final: 0.9075 (mmm) REVERT: F 659 MET cc_start: 0.8592 (tmm) cc_final: 0.8301 (tmm) REVERT: F 726 MET cc_start: 0.9518 (tpt) cc_final: 0.9057 (tpp) REVERT: F 774 MET cc_start: 0.9649 (mmp) cc_final: 0.9400 (mmm) REVERT: F 821 MET cc_start: 0.9383 (tpt) cc_final: 0.8836 (tpt) REVERT: G 778 MET cc_start: 0.8134 (mpp) cc_final: 0.6915 (pmm) REVERT: M 1957 MET cc_start: 0.8405 (ppp) cc_final: 0.8120 (ppp) REVERT: M 2062 MET cc_start: 0.9146 (mtm) cc_final: 0.8818 (ptm) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.6121 time to fit residues: 200.6527 Evaluate side-chains 180 residues out of total 7102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 5.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 494 optimal weight: 5.9990 chunk 662 optimal weight: 40.0000 chunk 190 optimal weight: 5.9990 chunk 573 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 622 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 639 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 691 ASN 5 203 ASN 5 499 GLN 5 581 ASN ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 GLN ** G 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.032643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.022429 restraints weight = 1140918.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.022666 restraints weight = 897044.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.022929 restraints weight = 717809.050| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 64722 Z= 0.237 Angle : 0.667 12.499 87675 Z= 0.350 Chirality : 0.043 0.232 10000 Planarity : 0.005 0.065 11151 Dihedral : 8.467 160.305 8872 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 36.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.55 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.10), residues: 7772 helix: 0.75 (0.09), residues: 3134 sheet: -0.88 (0.16), residues: 1060 loop : -1.14 (0.10), residues: 3578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 743 HIS 0.008 0.001 HIS 3 487 PHE 0.028 0.002 PHE 6 115 TYR 0.024 0.002 TYR 4 226 ARG 0.014 0.001 ARG 2 836 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8092.42 seconds wall clock time: 150 minutes 31.39 seconds (9031.39 seconds total)