Starting phenix.real_space_refine on Mon Dec 30 21:15:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kg8_37213/12_2024/8kg8_37213.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kg8_37213/12_2024/8kg8_37213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kg8_37213/12_2024/8kg8_37213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kg8_37213/12_2024/8kg8_37213.map" model { file = "/net/cci-nas-00/data/ceres_data/8kg8_37213/12_2024/8kg8_37213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kg8_37213/12_2024/8kg8_37213.cif" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 38 5.49 5 Mg 5 5.21 5 S 287 5.16 5 C 40440 2.51 5 N 10896 2.21 5 O 12156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 63829 Number of models: 1 Model: "" Number of chains: 25 Chain: "2" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5245 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 636} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5005 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 29, 'TRANS': 615} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "4" Number of atoms: 5503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5503 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 23, 'TRANS': 673} Chain breaks: 5 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "5" Number of atoms: 5334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5334 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 26, 'TRANS': 650} Chain breaks: 6 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "6" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4880 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 596} Chain breaks: 6 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "7" Number of atoms: 5023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5023 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 30, 'TRANS': 616} Chain breaks: 6 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1625 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1630 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain breaks: 1 Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1394 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2004 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 2 Chain: "E" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4591 Classifications: {'peptide': 568} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 552} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3467 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3362 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3358 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "M" Number of atoms: 6490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6490 Classifications: {'peptide': 813} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 29, 'TRANS': 783} Chain breaks: 6 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "N" Number of atoms: 4254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4254 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 30, 'TRANS': 505} Chain breaks: 5 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1311 SG CYS 2 341 91.581 160.591 137.576 1.00250.57 S ATOM 1334 SG CYS 2 344 92.389 164.084 137.802 1.00251.15 S ATOM 1492 SG CYS 2 364 94.913 160.439 138.719 1.00290.84 S ATOM 11648 SG CYS 4 349 104.028 156.934 175.174 1.00350.18 S ATOM 11669 SG CYS 4 352 107.295 157.715 176.962 1.00342.92 S ATOM 11816 SG CYS 4 371 104.003 158.634 178.580 1.00318.84 S ATOM 11858 SG CYS 4 376 105.315 160.483 175.427 1.00330.05 S ATOM 16893 SG CYS 5 183 66.756 160.436 138.520 1.00147.82 S ATOM 16918 SG CYS 5 186 65.162 163.736 138.383 1.00171.38 S ATOM 17082 SG CYS 5 211 68.999 163.699 138.682 1.00157.34 S ATOM 17119 SG CYS 5 236 67.042 162.656 141.580 1.00175.82 S ATOM 22315 SG CYS 6 311 108.580 158.676 151.903 1.00217.40 S ATOM 22337 SG CYS 6 314 108.780 162.347 151.610 1.00227.77 S ATOM 22494 SG CYS 6 333 108.097 160.683 155.180 1.00237.18 S ATOM 22528 SG CYS 6 338 105.507 160.705 152.510 1.00241.86 S ATOM 27560 SG CYS 7 262 76.562 156.169 182.939 1.00239.38 S ATOM 27733 SG CYS 7 284 74.842 158.228 182.207 1.00273.36 S ATOM 27770 SG CYS 7 289 76.893 160.493 181.745 1.00295.63 S ATOM 58502 SG CYS M2108 96.615 48.289 68.893 1.00202.50 S ATOM 58529 SG CYS M2111 98.151 45.719 71.122 1.00195.40 S ATOM 58678 SG CYS M2130 99.474 49.259 71.254 1.00182.05 S ATOM 58702 SG CYS M2133 100.225 46.982 68.292 1.00172.75 S ATOM 58965 SG CYS M2164 75.127 77.008 100.357 1.00198.58 S ATOM 58988 SG CYS M2167 74.845 74.668 103.299 1.00185.57 S ATOM 59089 SG CYS M2179 71.689 75.638 101.306 1.00207.17 S ATOM 59102 SG CYS M2181 73.493 78.085 103.629 1.00213.20 S Time building chain proxies: 27.24, per 1000 atoms: 0.43 Number of scatterers: 63829 At special positions: 0 Unit cell: (153.7, 244.86, 231.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 287 16.00 P 38 15.00 Mg 5 11.99 O 12156 8.00 N 10896 7.00 C 40440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.46 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 344 " pdb=" ZN 41400 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41400 " - pdb=" SG CYS 4 371 " pdb=" ZN 5 801 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 211 " pdb=" ZN 61101 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 289 " pdb=" ZN M3001 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2111 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2133 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2130 " pdb="ZN ZN M3001 " - pdb=" SG CYS M2108 " pdb=" ZN M3002 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2181 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2167 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2164 " pdb="ZN ZN M3002 " - pdb=" SG CYS M2179 " Number of angles added : 30 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15140 Finding SS restraints... Secondary structure from input PDB file: 290 helices and 81 sheets defined 45.0% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 Processing helix chain '2' and resid 193 through 199 Processing helix chain '2' and resid 200 through 218 Processing helix chain '2' and resid 225 through 238 removed outlier: 3.606A pdb=" N ALA 2 229 " --> pdb=" O SER 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 252 Processing helix chain '2' and resid 253 through 263 removed outlier: 3.811A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 4.376A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 289 Processing helix chain '2' and resid 310 through 314 Processing helix chain '2' and resid 435 through 443 removed outlier: 3.616A pdb=" N ASN 2 439 " --> pdb=" O ASP 2 435 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 489 Processing helix chain '2' and resid 492 through 500 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 Processing helix chain '2' and resid 572 through 577 removed outlier: 3.708A pdb=" N THR 2 577 " --> pdb=" O ALA 2 573 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 613 through 618 Processing helix chain '2' and resid 620 through 625 Processing helix chain '2' and resid 652 through 656 removed outlier: 3.744A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 Processing helix chain '2' and resid 670 through 677 removed outlier: 4.214A pdb=" N PHE 2 677 " --> pdb=" O ILE 2 673 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 706 Processing helix chain '2' and resid 739 through 756 removed outlier: 3.699A pdb=" N GLU 2 754 " --> pdb=" O LYS 2 750 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE 2 755 " --> pdb=" O LYS 2 751 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 774 removed outlier: 3.834A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 782 through 799 removed outlier: 3.715A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 3.532A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 848 Processing helix chain '2' and resid 850 through 862 removed outlier: 4.088A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 35 Processing helix chain '3' and resid 35 through 55 removed outlier: 4.347A pdb=" N ARG 3 39 " --> pdb=" O PHE 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 107 Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 121 through 136 Processing helix chain '3' and resid 161 through 163 No H-bonds generated for 'chain '3' and resid 161 through 163' Processing helix chain '3' and resid 172 through 176 Processing helix chain '3' and resid 281 through 283 No H-bonds generated for 'chain '3' and resid 281 through 283' Processing helix chain '3' and resid 343 through 355 removed outlier: 3.620A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 368 removed outlier: 4.507A pdb=" N ALA 3 368 " --> pdb=" O SER 3 364 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 386 removed outlier: 3.504A pdb=" N MET 3 386 " --> pdb=" O LEU 3 382 " (cutoff:3.500A) Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 438 through 443 Processing helix chain '3' and resid 474 through 478 Processing helix chain '3' and resid 479 through 493 removed outlier: 3.592A pdb=" N VAL 3 484 " --> pdb=" O ASP 3 480 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE 3 486 " --> pdb=" O ASP 3 482 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 542 removed outlier: 3.886A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 570 Processing helix chain '3' and resid 652 through 667 Processing helix chain '3' and resid 672 through 688 removed outlier: 3.749A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 690 through 694 removed outlier: 4.219A pdb=" N LYS 3 694 " --> pdb=" O ASN 3 691 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 716 removed outlier: 3.995A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 186 through 199 removed outlier: 3.679A pdb=" N CYS 4 190 " --> pdb=" O SER 4 186 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET 4 199 " --> pdb=" O ARG 4 195 " (cutoff:3.500A) Processing helix chain '4' and resid 202 through 210 removed outlier: 4.052A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 245 through 251 removed outlier: 3.792A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 Processing helix chain '4' and resid 264 through 287 Processing helix chain '4' and resid 292 through 299 Processing helix chain '4' and resid 313 through 317 Processing helix chain '4' and resid 318 through 322 removed outlier: 3.956A pdb=" N ILE 4 322 " --> pdb=" O PRO 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 386 through 389 Processing helix chain '4' and resid 502 through 515 Processing helix chain '4' and resid 517 through 527 removed outlier: 3.884A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 571 through 585 removed outlier: 4.090A pdb=" N SER 4 575 " --> pdb=" O SER 4 571 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 609 through 612 Processing helix chain '4' and resid 638 through 651 Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 701 Processing helix chain '4' and resid 713 through 731 removed outlier: 3.507A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) Processing helix chain '4' and resid 746 through 758 removed outlier: 4.308A pdb=" N SER 4 752 " --> pdb=" O THR 4 748 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 782 Processing helix chain '4' and resid 794 through 811 Processing helix chain '4' and resid 812 through 814 No H-bonds generated for 'chain '4' and resid 812 through 814' Processing helix chain '4' and resid 818 through 837 removed outlier: 3.634A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) Processing helix chain '4' and resid 851 through 874 removed outlier: 4.378A pdb=" N ILE 4 857 " --> pdb=" O GLY 4 853 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU 4 863 " --> pdb=" O ARG 4 859 " (cutoff:3.500A) Processing helix chain '4' and resid 882 through 889 Processing helix chain '4' and resid 900 through 913 removed outlier: 3.942A pdb=" N GLN 4 904 " --> pdb=" O SER 4 900 " (cutoff:3.500A) Processing helix chain '5' and resid 21 through 38 Processing helix chain '5' and resid 44 through 56 Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 72 through 82 removed outlier: 3.596A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU 5 82 " --> pdb=" O LYS 5 78 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 103 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 147 through 151 Processing helix chain '5' and resid 261 through 265 removed outlier: 3.530A pdb=" N VAL 5 265 " --> pdb=" O PRO 5 262 " (cutoff:3.500A) Processing helix chain '5' and resid 279 through 283 Processing helix chain '5' and resid 339 through 344 removed outlier: 4.023A pdb=" N TRP 5 343 " --> pdb=" O THR 5 339 " (cutoff:3.500A) Processing helix chain '5' and resid 350 through 362 Processing helix chain '5' and resid 365 through 373 Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 Processing helix chain '5' and resid 445 through 450 removed outlier: 3.520A pdb=" N THR 5 450 " --> pdb=" O ALA 5 446 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 481 through 485 Processing helix chain '5' and resid 486 through 491 removed outlier: 3.563A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) Processing helix chain '5' and resid 493 through 500 removed outlier: 3.607A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 540 Processing helix chain '5' and resid 543 through 550 removed outlier: 3.592A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) Processing helix chain '5' and resid 561 through 577 Processing helix chain '5' and resid 578 through 590 removed outlier: 3.766A pdb=" N ALA 5 582 " --> pdb=" O GLY 5 578 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 641 Processing helix chain '5' and resid 649 through 667 removed outlier: 3.577A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 693 removed outlier: 3.843A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) Processing helix chain '5' and resid 708 through 722 Processing helix chain '5' and resid 730 through 737 Processing helix chain '5' and resid 749 through 758 removed outlier: 4.215A pdb=" N TYR 5 753 " --> pdb=" O ASP 5 749 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 121 Processing helix chain '6' and resid 134 through 147 Processing helix chain '6' and resid 155 through 161 Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 364 through 368 Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 406 through 411 Processing helix chain '6' and resid 500 through 507 Processing helix chain '6' and resid 509 through 522 Processing helix chain '6' and resid 524 through 533 Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 592 Processing helix chain '6' and resid 626 through 631 removed outlier: 3.832A pdb=" N LEU 6 630 " --> pdb=" O GLY 6 626 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA 6 631 " --> pdb=" O ALA 6 627 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 626 through 631' Processing helix chain '6' and resid 645 through 650 Processing helix chain '6' and resid 651 through 653 No H-bonds generated for 'chain '6' and resid 651 through 653' Processing helix chain '6' and resid 702 through 707 Processing helix chain '6' and resid 720 through 737 Processing helix chain '6' and resid 747 through 760 removed outlier: 3.562A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR 6 754 " --> pdb=" O GLN 6 750 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 784 Processing helix chain '6' and resid 796 through 814 removed outlier: 3.579A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 836 Processing helix chain '7' and resid 13 through 27 Processing helix chain '7' and resid 61 through 72 Processing helix chain '7' and resid 82 through 95 removed outlier: 3.612A pdb=" N LEU 7 94 " --> pdb=" O ASN 7 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN 7 95 " --> pdb=" O GLU 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 101 through 107 removed outlier: 3.724A pdb=" N GLN 7 107 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 124 removed outlier: 4.029A pdb=" N PHE 7 113 " --> pdb=" O ASN 7 109 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 155 removed outlier: 4.059A pdb=" N MET 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) Processing helix chain '7' and resid 231 through 235 Processing helix chain '7' and resid 286 through 293 Processing helix chain '7' and resid 319 through 322 removed outlier: 3.520A pdb=" N VAL 7 322 " --> pdb=" O SER 7 319 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 319 through 322' Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 363 through 369 removed outlier: 3.502A pdb=" N LYS 7 367 " --> pdb=" O PHE 7 363 " (cutoff:3.500A) Processing helix chain '7' and resid 396 through 408 Processing helix chain '7' and resid 409 through 419 removed outlier: 4.053A pdb=" N ALA 7 415 " --> pdb=" O TYR 7 411 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA 7 419 " --> pdb=" O ALA 7 415 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 513 through 517 Processing helix chain '7' and resid 530 through 542 Processing helix chain '7' and resid 579 through 584 removed outlier: 3.584A pdb=" N ILE 7 584 " --> pdb=" O PRO 7 580 " (cutoff:3.500A) Processing helix chain '7' and resid 587 through 594 removed outlier: 3.522A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 607 through 623 Processing helix chain '7' and resid 635 through 649 removed outlier: 4.355A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 675 Processing helix chain '7' and resid 679 through 683 Processing helix chain '7' and resid 685 through 703 Processing helix chain '7' and resid 709 through 728 removed outlier: 3.554A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 22 Processing helix chain 'A' and resid 33 through 61 Processing helix chain 'A' and resid 64 through 105 removed outlier: 3.510A pdb=" N ALA A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.686A pdb=" N ASN A 122 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.505A pdb=" N ASP A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 203 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'B' and resid 94 through 108 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 137 through 161 removed outlier: 3.658A pdb=" N GLY B 143 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 200 removed outlier: 3.627A pdb=" N ILE B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 3.527A pdb=" N GLU B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.568A pdb=" N GLY C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.964A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 117 through 140 removed outlier: 3.547A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 167 Processing helix chain 'C' and resid 170 through 192 Processing helix chain 'D' and resid 5 through 13 Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.507A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 106 Processing helix chain 'D' and resid 123 through 154 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 176 through 198 Processing helix chain 'D' and resid 199 through 202 Processing helix chain 'D' and resid 203 through 207 Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 279 through 288 removed outlier: 4.546A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 6 No H-bonds generated for 'chain 'E' and resid 4 through 6' Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.644A pdb=" N ALA E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 52 Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 99 through 103 removed outlier: 4.044A pdb=" N TYR E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 103' Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 152 through 166 Processing helix chain 'E' and resid 224 through 241 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 284 through 303 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 328 through 332 Processing helix chain 'E' and resid 333 through 341 Processing helix chain 'E' and resid 341 through 349 Processing helix chain 'E' and resid 352 through 366 removed outlier: 4.126A pdb=" N LYS E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 375 Processing helix chain 'E' and resid 381 through 395 removed outlier: 6.351A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 400 Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 464 through 483 removed outlier: 3.715A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 517 Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 541 through 558 removed outlier: 3.563A pdb=" N GLU E 558 " --> pdb=" O GLU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 599 removed outlier: 3.778A pdb=" N LYS E 599 " --> pdb=" O ILE E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 615 removed outlier: 3.872A pdb=" N ALA E 608 " --> pdb=" O ASN E 604 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU E 615 " --> pdb=" O GLN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 647 removed outlier: 4.682A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'F' and resid 672 through 680 removed outlier: 4.182A pdb=" N TYR F 676 " --> pdb=" O ALA F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 716 removed outlier: 4.012A pdb=" N SER F 716 " --> pdb=" O PRO F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 732 Processing helix chain 'F' and resid 782 through 787 Processing helix chain 'F' and resid 818 through 843 removed outlier: 3.894A pdb=" N GLU F 824 " --> pdb=" O SER F 820 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU F 842 " --> pdb=" O THR F 838 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 876 removed outlier: 3.502A pdb=" N ASP F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 887 removed outlier: 3.619A pdb=" N HIS F 887 " --> pdb=" O LEU F 883 " (cutoff:3.500A) Processing helix chain 'F' and resid 891 through 905 Processing helix chain 'F' and resid 907 through 923 removed outlier: 3.791A pdb=" N LYS F 912 " --> pdb=" O PRO F 908 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 913 " --> pdb=" O SER F 909 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU F 923 " --> pdb=" O GLU F 919 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 680 Processing helix chain 'G' and resid 724 through 733 removed outlier: 4.267A pdb=" N SER G 732 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY G 733 " --> pdb=" O TRP G 729 " (cutoff:3.500A) Processing helix chain 'G' and resid 782 through 787 Processing helix chain 'G' and resid 818 through 844 removed outlier: 3.979A pdb=" N GLU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU G 835 " --> pdb=" O LYS G 831 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU G 836 " --> pdb=" O VAL G 832 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR G 840 " --> pdb=" O LEU G 836 " (cutoff:3.500A) Processing helix chain 'G' and resid 850 through 877 Processing helix chain 'G' and resid 878 through 888 removed outlier: 3.916A pdb=" N GLU G 888 " --> pdb=" O SER G 884 " (cutoff:3.500A) Processing helix chain 'G' and resid 891 through 903 Processing helix chain 'G' and resid 907 through 922 removed outlier: 3.764A pdb=" N VAL G 911 " --> pdb=" O LEU G 907 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS G 912 " --> pdb=" O PRO G 908 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 913 " --> pdb=" O SER G 909 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE G 914 " --> pdb=" O LEU G 910 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR G 922 " --> pdb=" O ARG G 918 " (cutoff:3.500A) Processing helix chain 'H' and resid 673 through 680 Processing helix chain 'H' and resid 724 through 733 removed outlier: 4.248A pdb=" N TRP H 729 " --> pdb=" O ASN H 725 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS H 730 " --> pdb=" O MET H 726 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER H 732 " --> pdb=" O ILE H 728 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY H 733 " --> pdb=" O TRP H 729 " (cutoff:3.500A) Processing helix chain 'H' and resid 818 through 843 removed outlier: 3.709A pdb=" N GLU H 824 " --> pdb=" O SER H 820 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU H 835 " --> pdb=" O LYS H 831 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU H 836 " --> pdb=" O VAL H 832 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR H 840 " --> pdb=" O LEU H 836 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU H 841 " --> pdb=" O LEU H 837 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN H 843 " --> pdb=" O ASP H 839 " (cutoff:3.500A) Processing helix chain 'H' and resid 850 through 876 Processing helix chain 'H' and resid 878 through 886 Processing helix chain 'H' and resid 891 through 905 Processing helix chain 'H' and resid 907 through 923 Processing helix chain 'M' and resid 1376 through 1380 removed outlier: 3.822A pdb=" N SER M1379 " --> pdb=" O ILE M1376 " (cutoff:3.500A) Processing helix chain 'M' and resid 1408 through 1412 removed outlier: 3.570A pdb=" N GLU M1412 " --> pdb=" O GLU M1409 " (cutoff:3.500A) Processing helix chain 'M' and resid 1436 through 1442 Processing helix chain 'M' and resid 1451 through 1462 removed outlier: 3.604A pdb=" N GLN M1460 " --> pdb=" O GLY M1456 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN M1461 " --> pdb=" O LYS M1457 " (cutoff:3.500A) Processing helix chain 'M' and resid 1525 through 1547 removed outlier: 4.406A pdb=" N MET M1535 " --> pdb=" O ILE M1531 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS M1538 " --> pdb=" O GLN M1534 " (cutoff:3.500A) Processing helix chain 'M' and resid 1565 through 1570 Processing helix chain 'M' and resid 1570 through 1584 Processing helix chain 'M' and resid 1597 through 1603 removed outlier: 4.107A pdb=" N THR M1603 " --> pdb=" O LYS M1599 " (cutoff:3.500A) Processing helix chain 'M' and resid 1603 through 1608 Processing helix chain 'M' and resid 1629 through 1641 removed outlier: 3.727A pdb=" N LYS M1634 " --> pdb=" O THR M1630 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU M1635 " --> pdb=" O LEU M1631 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL M1636 " --> pdb=" O LEU M1632 " (cutoff:3.500A) Processing helix chain 'M' and resid 1641 through 1656 removed outlier: 4.151A pdb=" N TRP M1645 " --> pdb=" O SER M1641 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE M1646 " --> pdb=" O SER M1642 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER M1647 " --> pdb=" O GLY M1643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS M1648 " --> pdb=" O SER M1644 " (cutoff:3.500A) Processing helix chain 'M' and resid 1666 through 1683 removed outlier: 3.583A pdb=" N TYR M1670 " --> pdb=" O ASP M1666 " (cutoff:3.500A) Processing helix chain 'M' and resid 1700 through 1704 removed outlier: 3.542A pdb=" N ASN M1703 " --> pdb=" O GLY M1700 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP M1704 " --> pdb=" O ILE M1701 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1700 through 1704' Processing helix chain 'M' and resid 1706 through 1714 Processing helix chain 'M' and resid 1738 through 1747 Processing helix chain 'M' and resid 1784 through 1804 removed outlier: 3.705A pdb=" N LYS M1804 " --> pdb=" O ASP M1800 " (cutoff:3.500A) Processing helix chain 'M' and resid 1806 through 1818 removed outlier: 3.622A pdb=" N ASP M1810 " --> pdb=" O ASN M1806 " (cutoff:3.500A) Processing helix chain 'M' and resid 1829 through 1855 Processing helix chain 'M' and resid 1875 through 1877 No H-bonds generated for 'chain 'M' and resid 1875 through 1877' Processing helix chain 'M' and resid 1878 through 1891 Processing helix chain 'M' and resid 1892 through 1896 Processing helix chain 'M' and resid 1941 through 1945 Processing helix chain 'M' and resid 1949 through 1976 Processing helix chain 'M' and resid 2002 through 2006 Processing helix chain 'M' and resid 2007 through 2026 Processing helix chain 'M' and resid 2049 through 2063 Processing helix chain 'M' and resid 2068 through 2083 removed outlier: 3.681A pdb=" N PHE M2083 " --> pdb=" O LEU M2079 " (cutoff:3.500A) Processing helix chain 'M' and resid 2123 through 2128 Processing helix chain 'M' and resid 2138 through 2159 Processing helix chain 'M' and resid 2190 through 2209 Processing helix chain 'M' and resid 2210 through 2221 Processing helix chain 'N' and resid 13 through 30 removed outlier: 3.605A pdb=" N LEU N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Proline residue: N 19 - end of helix removed outlier: 3.972A pdb=" N ARG N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 49 Processing helix chain 'N' and resid 55 through 70 Processing helix chain 'N' and resid 79 through 96 Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 174 through 178 removed outlier: 4.003A pdb=" N GLN N 178 " --> pdb=" O ALA N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 237 removed outlier: 4.771A pdb=" N PHE N 218 " --> pdb=" O LYS N 214 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU N 219 " --> pdb=" O VAL N 215 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG N 221 " --> pdb=" O MET N 217 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN N 234 " --> pdb=" O MET N 230 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE N 235 " --> pdb=" O ARG N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 275 removed outlier: 3.802A pdb=" N LEU N 275 " --> pdb=" O LYS N 272 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 360 Processing helix chain 'N' and resid 381 through 394 Processing helix chain 'N' and resid 410 through 427 removed outlier: 3.581A pdb=" N ASP N 426 " --> pdb=" O GLN N 422 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP N 427 " --> pdb=" O LYS N 423 " (cutoff:3.500A) Processing helix chain 'N' and resid 453 through 470 Processing helix chain 'N' and resid 509 through 512 Processing helix chain 'N' and resid 513 through 520 removed outlier: 3.501A pdb=" N CYS N 520 " --> pdb=" O ILE N 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 545 through 554 removed outlier: 3.708A pdb=" N ARG N 549 " --> pdb=" O ASP N 545 " (cutoff:3.500A) Processing helix chain 'N' and resid 595 through 610 Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 242 Processing sheet with id=AA2, first strand: chain '2' and resid 303 through 304 removed outlier: 7.188A pdb=" N TYR 2 304 " --> pdb=" O THR 2 321 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N VAL 2 323 " --> pdb=" O TYR 2 304 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 317 through 327 current: chain '2' and resid 382 through 391 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 405 through 410 current: chain '2' and resid 448 through 458 Processing sheet with id=AA3, first strand: chain '2' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain '2' and resid 339 through 341 removed outlier: 4.087A pdb=" N ARG 2 374 " --> pdb=" O ASN 2 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 526 through 527 Processing sheet with id=AA6, first strand: chain '2' and resid 563 through 567 removed outlier: 6.449A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA 2 566 " --> pdb=" O ASP 2 607 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL 2 539 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA 2 650 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 578 through 582 Processing sheet with id=AA8, first strand: chain '2' and resid 628 through 633 Processing sheet with id=AA9, first strand: chain '3' and resid 95 through 99 Processing sheet with id=AB1, first strand: chain '3' and resid 165 through 166 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 179 through 189 current: chain '3' and resid 209 through 213 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 209 through 213 current: chain '3' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 273 through 279 current: chain '3' and resid 318 through 327 Processing sheet with id=AB2, first strand: chain '3' and resid 329 through 330 removed outlier: 4.607A pdb=" N VAL 3 336 " --> pdb=" O HIS 3 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 429 through 433 removed outlier: 6.359A pdb=" N ILE 3 430 " --> pdb=" O CYS 3 471 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP 3 473 " --> pdb=" O ILE 3 430 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 444 through 448 Processing sheet with id=AB5, first strand: chain '3' and resid 494 through 499 Processing sheet with id=AB6, first strand: chain '4' and resid 324 through 335 removed outlier: 6.632A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N SER 4 414 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N VAL 4 461 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N SER 4 416 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL 4 463 " --> pdb=" O SER 4 416 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS 4 418 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N HIS 4 465 " --> pdb=" O CYS 4 418 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR 4 436 " --> pdb=" O VAL 4 464 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL 4 466 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU 4 434 " --> pdb=" O VAL 4 466 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS 4 324 " --> pdb=" O PHE 4 439 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 339 through 344 removed outlier: 6.710A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 355 through 356 Processing sheet with id=AB9, first strand: chain '4' and resid 444 through 445 removed outlier: 4.312A pdb=" N ILE 4 444 " --> pdb=" O LYS 4 454 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 590 through 592 removed outlier: 3.770A pdb=" N LEU 4 672 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN 4 563 " --> pdb=" O LEU 4 704 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N TYR 4 706 " --> pdb=" O ASN 4 563 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 604 through 607 Processing sheet with id=AC3, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC4, first strand: chain '4' and resid 916 through 918 Processing sheet with id=AC5, first strand: chain '5' and resid 60 through 64 Processing sheet with id=AC6, first strand: chain '5' and resid 159 through 169 removed outlier: 6.537A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE 5 330 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 173 through 183 Processing sheet with id=AC8, first strand: chain '5' and resid 398 through 399 Processing sheet with id=AC9, first strand: chain '5' and resid 436 through 439 removed outlier: 6.135A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 451 through 455 Processing sheet with id=AD2, first strand: chain '5' and resid 501 through 506 Processing sheet with id=AD3, first strand: chain '5' and resid 613 through 614 removed outlier: 6.895A pdb=" N ARG 5 613 " --> pdb=" O ALA 5 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain '5' and resid 727 through 729 Processing sheet with id=AD5, first strand: chain '6' and resid 150 through 154 Processing sheet with id=AD6, first strand: chain '6' and resid 287 through 288 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 287 through 288 current: chain '6' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 317 through 322 current: chain '6' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 376 through 382 current: chain '6' and resid 450 through 461 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '6' and resid 437 through 438 Processing sheet with id=AD8, first strand: chain '6' and resid 596 through 599 removed outlier: 6.263A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 610 through 614 Processing sheet with id=AE1, first strand: chain '6' and resid 660 through 664 Processing sheet with id=AE2, first strand: chain '6' and resid 764 through 765 removed outlier: 6.970A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain '7' and resid 78 through 81 removed outlier: 5.993A pdb=" N VAL 7 78 " --> pdb=" O TYR 7 203 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS 7 205 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE 7 80 " --> pdb=" O LYS 7 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain '7' and resid 238 through 248 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 248 current: chain '7' and resid 268 through 272 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 268 through 272 current: chain '7' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 330 through 336 current: chain '7' and resid 375 through 383 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain '7' and resid 481 through 484 removed outlier: 6.930A pdb=" N VAL 7 456 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS 7 457 " --> pdb=" O ILE 7 596 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '7' and resid 545 through 547 Processing sheet with id=AE7, first strand: chain 'A' and resid 162 through 166 removed outlier: 3.588A pdb=" N SER E 56 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 172 through 174 removed outlier: 4.029A pdb=" N GLY A 172 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 24 through 27 Processing sheet with id=AF1, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AF2, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AF3, first strand: chain 'D' and resid 247 through 248 Processing sheet with id=AF4, first strand: chain 'E' and resid 104 through 105 removed outlier: 3.903A pdb=" N SER E 115 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 316 through 322 Processing sheet with id=AF6, first strand: chain 'E' and resid 526 through 530 removed outlier: 3.899A pdb=" N ILE E 572 " --> pdb=" O LEU E 530 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER E 571 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 492 through 496 removed outlier: 6.651A pdb=" N VAL F 502 " --> pdb=" O LEU F 494 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N MET F 496 " --> pdb=" O GLY F 500 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY F 500 " --> pdb=" O MET F 496 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 536 through 538 Processing sheet with id=AF9, first strand: chain 'F' and resid 581 through 583 Processing sheet with id=AG1, first strand: chain 'F' and resid 615 through 620 removed outlier: 4.069A pdb=" N ALA F 617 " --> pdb=" O VAL F 628 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 684 through 686 removed outlier: 7.114A pdb=" N PHE F 698 " --> pdb=" O LYS F 685 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY F 699 " --> pdb=" O THR F 703 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR F 703 " --> pdb=" O GLY F 699 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU F 704 " --> pdb=" O ILE F 721 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 740 through 748 removed outlier: 6.977A pdb=" N ASN F 753 " --> pdb=" O LEU F 745 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU F 747 " --> pdb=" O THR F 751 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR F 751 " --> pdb=" O LEU F 747 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.563A pdb=" N VAL G 502 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N MET G 496 " --> pdb=" O GLY G 500 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY G 500 " --> pdb=" O MET G 496 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE G 513 " --> pdb=" O PHE G 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE G 528 " --> pdb=" O ILE G 513 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL G 515 " --> pdb=" O TYR G 526 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR G 526 " --> pdb=" O VAL G 515 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 536 through 539 Processing sheet with id=AG6, first strand: chain 'G' and resid 578 through 583 removed outlier: 3.812A pdb=" N SER G 580 " --> pdb=" O GLY G 591 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 615 through 620 removed outlier: 7.117A pdb=" N VAL G 628 " --> pdb=" O VAL G 616 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU G 618 " --> pdb=" O PHE G 626 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE G 626 " --> pdb=" O LEU G 618 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU G 640 " --> pdb=" O ARG G 653 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG G 653 " --> pdb=" O LEU G 640 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N GLU G 642 " --> pdb=" O TYR G 651 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR G 651 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 684 through 686 removed outlier: 4.291A pdb=" N GLY G 699 " --> pdb=" O THR G 703 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR G 703 " --> pdb=" O GLY G 699 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 722 " --> pdb=" O LEU G 704 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU G 706 " --> pdb=" O PRO G 720 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 742 through 744 Processing sheet with id=AH1, first strand: chain 'H' and resid 492 through 496 removed outlier: 6.827A pdb=" N VAL H 502 " --> pdb=" O LEU H 494 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 536 through 540 removed outlier: 3.668A pdb=" N GLY H 543 " --> pdb=" O ASN H 540 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 580 through 583 removed outlier: 3.677A pdb=" N SER H 580 " --> pdb=" O GLY H 591 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 615 through 620 removed outlier: 3.959A pdb=" N ALA H 617 " --> pdb=" O VAL H 628 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 619 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR H 638 " --> pdb=" O ARG H 653 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG H 653 " --> pdb=" O TYR H 638 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU H 640 " --> pdb=" O TYR H 651 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 703 through 706 removed outlier: 6.210A pdb=" N LEU H 704 " --> pdb=" O ILE H 721 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 743 through 747 removed outlier: 6.528A pdb=" N ASN H 753 " --> pdb=" O LEU H 745 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 1320 through 1321 removed outlier: 3.564A pdb=" N THR M1446 " --> pdb=" O SER M1320 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET M1470 " --> pdb=" O PHE M1447 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 1337 through 1341 removed outlier: 9.204A pdb=" N PHE M1463 " --> pdb=" O ASN M1348 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR M1350 " --> pdb=" O PHE M1463 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 1484 through 1488 removed outlier: 3.622A pdb=" N GLN M1593 " --> pdb=" O LEU M1487 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU M1590 " --> pdb=" O VAL M1613 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 1508 through 1511 removed outlier: 3.686A pdb=" N ILE M1509 " --> pdb=" O ASN M1557 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 1721 through 1722 removed outlier: 6.363A pdb=" N LEU M1867 " --> pdb=" O VAL M1859 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA M1861 " --> pdb=" O GLN M1865 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN M1865 " --> pdb=" O ALA M1861 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL M1731 " --> pdb=" O TYR M1905 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR M1905 " --> pdb=" O VAL M1731 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP M1733 " --> pdb=" O LYS M1903 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP M1899 " --> pdb=" O ASP M1737 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 1725 through 1727 removed outlier: 3.784A pdb=" N LEU M1909 " --> pdb=" O TYR M1727 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU M1908 " --> pdb=" O LEU M1920 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 2102 through 2107 removed outlier: 6.324A pdb=" N ILE M2117 " --> pdb=" O PRO M2104 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 2162 through 2164 Processing sheet with id=AI6, first strand: chain 'N' and resid 172 through 173 removed outlier: 6.744A pdb=" N VAL N 540 " --> pdb=" O VAL N 640 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N CYS N 642 " --> pdb=" O VAL N 540 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE N 542 " --> pdb=" O CYS N 642 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 181 through 184 Processing sheet with id=AI8, first strand: chain 'N' and resid 313 through 314 removed outlier: 5.395A pdb=" N PHE N 339 " --> pdb=" O TYR N 333 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR N 333 " --> pdb=" O PHE N 339 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL N 341 " --> pdb=" O ILE N 331 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE N 331 " --> pdb=" O VAL N 341 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP N 296 " --> pdb=" O ILE N 307 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N PHE N 339 " --> pdb=" O SER N 304 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU N 306 " --> pdb=" O PHE N 339 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL N 341 " --> pdb=" O GLU N 306 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP N 308 " --> pdb=" O VAL N 341 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER N 343 " --> pdb=" O ASP N 308 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 523 through 525 removed outlier: 6.089A pdb=" N MET N 481 " --> pdb=" O VAL N 524 " (cutoff:3.500A) 2795 hydrogen bonds defined for protein. 7980 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: 31.33 Time building geometry restraints manager: 14.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 21075 1.36 - 1.51: 16781 1.51 - 1.65: 26729 1.65 - 1.80: 270 1.80 - 1.95: 193 Bond restraints: 65048 Sorted by residual: bond pdb=" CA PRO A 157 " pdb=" C PRO A 157 " ideal model delta sigma weight residual 1.517 1.495 0.022 9.30e-03 1.16e+04 5.46e+00 bond pdb=" C VAL 6 300 " pdb=" N ARG 6 301 " ideal model delta sigma weight residual 1.327 1.356 -0.029 1.71e-02 3.42e+03 2.96e+00 bond pdb=" C MET M1610 " pdb=" N PRO M1611 " ideal model delta sigma weight residual 1.331 1.348 -0.017 1.27e-02 6.20e+03 1.86e+00 bond pdb=" C ARG N 18 " pdb=" N PRO N 19 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.75e+00 bond pdb=" CA THR 3 87 " pdb=" CB THR 3 87 " ideal model delta sigma weight residual 1.522 1.540 -0.017 1.32e-02 5.74e+03 1.70e+00 ... (remaining 65043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 86593 1.84 - 3.68: 1354 3.68 - 5.52: 148 5.52 - 7.36: 28 7.36 - 9.20: 13 Bond angle restraints: 88136 Sorted by residual: angle pdb=" N VAL H 780 " pdb=" CA VAL H 780 " pdb=" C VAL H 780 " ideal model delta sigma weight residual 113.42 108.37 5.05 1.17e+00 7.31e-01 1.86e+01 angle pdb=" N ILE 3 197 " pdb=" CA ILE 3 197 " pdb=" C ILE 3 197 " ideal model delta sigma weight residual 113.71 109.65 4.06 9.50e-01 1.11e+00 1.82e+01 angle pdb=" C MET 6 313 " pdb=" N CYS 6 314 " pdb=" CA CYS 6 314 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C SER 5 341 " pdb=" CA SER 5 341 " pdb=" CB SER 5 341 " ideal model delta sigma weight residual 115.89 110.86 5.03 1.32e+00 5.74e-01 1.45e+01 angle pdb=" N ILE M1660 " pdb=" CA ILE M1660 " pdb=" C ILE M1660 " ideal model delta sigma weight residual 112.80 108.45 4.35 1.15e+00 7.56e-01 1.43e+01 ... (remaining 88131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 38830 35.97 - 71.94: 722 71.94 - 107.92: 47 107.92 - 143.89: 3 143.89 - 179.86: 3 Dihedral angle restraints: 39605 sinusoidal: 16293 harmonic: 23312 Sorted by residual: dihedral pdb=" C5' ADP 31001 " pdb=" O5' ADP 31001 " pdb=" PA ADP 31001 " pdb=" O2A ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 119.86 -179.86 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PA ADP 31001 " pdb=" PB ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 95.07 -155.07 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O1B ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PB ADP 31001 " pdb=" PA ADP 31001 " ideal model delta sinusoidal sigma weight residual -60.00 63.21 -123.22 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 39602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 7930 0.048 - 0.095: 1699 0.095 - 0.142: 424 0.142 - 0.190: 12 0.190 - 0.237: 1 Chirality restraints: 10066 Sorted by residual: chirality pdb=" CA MET B 1 " pdb=" N MET B 1 " pdb=" C MET B 1 " pdb=" CB MET B 1 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE G 740 " pdb=" CA ILE G 740 " pdb=" CG1 ILE G 740 " pdb=" CG2 ILE G 740 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CB ILE H 740 " pdb=" CA ILE H 740 " pdb=" CG1 ILE H 740 " pdb=" CG2 ILE H 740 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 10063 not shown) Planarity restraints: 11194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 584 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO G 585 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 585 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 585 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 766 " 0.020 2.00e-02 2.50e+03 1.77e-02 5.45e+00 pdb=" CG PHE F 766 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE F 766 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE F 766 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 766 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 766 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 766 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 661 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO H 662 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 662 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 662 " -0.031 5.00e-02 4.00e+02 ... (remaining 11191 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 831 2.58 - 3.16: 54500 3.16 - 3.74: 106369 3.74 - 4.32: 142242 4.32 - 4.90: 232391 Nonbonded interactions: 536333 Sorted by model distance: nonbonded pdb=" OG SER 7 467 " pdb="MG MG 7 902 " model vdw 1.997 2.170 nonbonded pdb="MG MG 7 902 " pdb=" O2B AGS 7 903 " model vdw 2.025 2.170 nonbonded pdb=" O2B ADP 31001 " pdb="MG MG 31002 " model vdw 2.032 2.170 nonbonded pdb=" O3A AGS 5 802 " pdb="MG MG 5 803 " model vdw 2.035 2.170 nonbonded pdb=" OG SER 5 423 " pdb="MG MG 5 803 " model vdw 2.041 2.170 ... (remaining 536328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 474 through 490 or (resid 491 and (name N or name CA or na \ me C or name O or name CB )) or resid 492 through 576 or (resid 577 and (name N \ or name CA or name C or name O or name CB )) or resid 578 through 586 or (resid \ 587 and (name N or name CA or name C or name O or name CB )) or resid 588 throug \ h 665 or resid 670 through 782 or (resid 783 and (name N or name CA or name C or \ name O or name CB )) or resid 784 or resid 816 through 889 or (resid 890 and (n \ ame N or name CA or name C or name O or name CB )) or resid 891 through 899 or ( \ resid 900 and (name N or name CA or name C or name O or name CB )) or resid 901 \ or (resid 902 and (name N or name CA or name C or name O or name CB )) or resid \ 903 through 922)) selection = (chain 'G' and (resid 474 through 490 or (resid 491 and (name N or name CA or na \ me C or name O or name CB )) or resid 492 through 586 or (resid 587 and (name N \ or name CA or name C or name O or name CB )) or resid 588 through 665 or resid 6 \ 70 through 782 or (resid 783 and (name N or name CA or name C or name O or name \ CB )) or resid 784 or resid 816 through 901 or (resid 902 and (name N or name CA \ or name C or name O or name CB )) or resid 903 through 909 or (resid 910 and (n \ ame N or name CA or name C or name O or name CB )) or resid 911 through 922)) selection = (chain 'H' and (resid 474 through 576 or (resid 577 and (name N or name CA or na \ me C or name O or name CB )) or resid 578 through 784 or resid 816 through 889 o \ r (resid 890 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 91 through 899 or (resid 900 and (name N or name CA or name C or name O or name \ CB )) or resid 901 through 909 or (resid 910 and (name N or name CA or name C or \ name O or name CB )) or resid 911 through 922)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.350 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: 0.090 Extract box with map and model: 2.340 Check model and map are aligned: 0.440 Set scattering table: 0.530 Process input model: 129.750 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 65048 Z= 0.145 Angle : 0.578 9.203 88136 Z= 0.323 Chirality : 0.041 0.237 10066 Planarity : 0.004 0.065 11194 Dihedral : 14.463 179.860 24465 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.01 % Allowed : 0.23 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.10), residues: 7818 helix: 1.64 (0.09), residues: 3126 sheet: -1.14 (0.14), residues: 1315 loop : -0.74 (0.11), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 50 HIS 0.010 0.001 HIS 7 538 PHE 0.040 0.001 PHE F 766 TYR 0.020 0.001 TYR G 862 ARG 0.006 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 5.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8864 (pmm) cc_final: 0.8571 (ttp) REVERT: 3 306 MET cc_start: 0.9141 (tpp) cc_final: 0.8843 (tpp) REVERT: 4 272 MET cc_start: 0.9689 (mmm) cc_final: 0.9408 (tpp) REVERT: 4 780 MET cc_start: 0.8017 (ppp) cc_final: 0.7554 (ppp) REVERT: 5 270 MET cc_start: 0.8608 (ppp) cc_final: 0.8362 (ppp) REVERT: 5 276 MET cc_start: 0.9135 (pmm) cc_final: 0.8722 (pmm) REVERT: 6 373 MET cc_start: 0.8966 (tpp) cc_final: 0.8676 (tpp) REVERT: 6 629 MET cc_start: 0.9110 (mmp) cc_final: 0.8471 (mmm) REVERT: 6 656 MET cc_start: 0.9587 (ptm) cc_final: 0.8495 (ppp) REVERT: 6 736 MET cc_start: 0.8678 (mmp) cc_final: 0.8350 (mmm) REVERT: 7 66 MET cc_start: 0.9380 (mmp) cc_final: 0.9103 (mmp) REVERT: D 129 MET cc_start: 0.8702 (mpp) cc_final: 0.8042 (mpp) REVERT: G 774 MET cc_start: 0.9084 (tpt) cc_final: 0.8733 (tpt) REVERT: H 774 MET cc_start: 0.6732 (ptt) cc_final: 0.6298 (ptt) REVERT: M 1465 MET cc_start: 0.7030 (ppp) cc_final: 0.6808 (ppp) REVERT: M 1470 MET cc_start: 0.6701 (mpp) cc_final: 0.6474 (mpp) REVERT: M 1482 MET cc_start: 0.6935 (tpt) cc_final: 0.6642 (tpt) REVERT: M 1958 MET cc_start: 0.9115 (mpp) cc_final: 0.8769 (mpp) REVERT: N 217 MET cc_start: 0.9236 (ptm) cc_final: 0.8880 (ptm) REVERT: N 639 MET cc_start: 0.8272 (mmp) cc_final: 0.7839 (mmm) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.5651 time to fit residues: 198.2911 Evaluate side-chains 184 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 667 optimal weight: 50.0000 chunk 598 optimal weight: 5.9990 chunk 332 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 403 optimal weight: 7.9990 chunk 319 optimal weight: 4.9990 chunk 619 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 376 optimal weight: 0.9990 chunk 460 optimal weight: 8.9990 chunk 717 optimal weight: 0.4980 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 760 GLN 3 312 ASN 4 848 ASN ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 698 ASN ** 7 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 412 ASN ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 683 GLN A 71 GLN A 82 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN F 563 HIS F 843 ASN H 843 ASN ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1806 ASN M2022 GLN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 291 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 65048 Z= 0.231 Angle : 0.553 8.366 88136 Z= 0.292 Chirality : 0.041 0.170 10066 Planarity : 0.004 0.062 11194 Dihedral : 8.473 146.755 8948 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 7818 helix: 1.66 (0.09), residues: 3205 sheet: -1.15 (0.15), residues: 1282 loop : -0.78 (0.11), residues: 3331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 3 153 HIS 0.006 0.001 HIS G 629 PHE 0.034 0.001 PHE F 766 TYR 0.024 0.001 TYR G 862 ARG 0.006 0.000 ARG M1678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 5.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8839 (pmm) cc_final: 0.8565 (ttp) REVERT: 2 823 MET cc_start: 0.9184 (ptp) cc_final: 0.8922 (ptp) REVERT: 3 306 MET cc_start: 0.9104 (tpp) cc_final: 0.8826 (tpp) REVERT: 3 386 MET cc_start: 0.8751 (ppp) cc_final: 0.8422 (ppp) REVERT: 3 407 MET cc_start: 0.8514 (ppp) cc_final: 0.8137 (ppp) REVERT: 4 272 MET cc_start: 0.9714 (mmm) cc_final: 0.9431 (tpp) REVERT: 4 280 MET cc_start: 0.8711 (mmm) cc_final: 0.8259 (tpt) REVERT: 4 382 MET cc_start: 0.7973 (mpp) cc_final: 0.7492 (mpp) REVERT: 4 780 MET cc_start: 0.7862 (ppp) cc_final: 0.7566 (ppp) REVERT: 4 811 MET cc_start: 0.8888 (ppp) cc_final: 0.8681 (ppp) REVERT: 4 847 MET cc_start: 0.8002 (mpp) cc_final: 0.7711 (mpp) REVERT: 5 270 MET cc_start: 0.8697 (ppp) cc_final: 0.8460 (ppp) REVERT: 6 313 MET cc_start: 0.9385 (pmm) cc_final: 0.9143 (pmm) REVERT: 6 629 MET cc_start: 0.9164 (mmp) cc_final: 0.8477 (mmm) REVERT: 6 656 MET cc_start: 0.9582 (ptm) cc_final: 0.9003 (ptm) REVERT: 6 736 MET cc_start: 0.8715 (mmp) cc_final: 0.8385 (mmm) REVERT: 7 66 MET cc_start: 0.9406 (mmp) cc_final: 0.8961 (mmp) REVERT: 7 125 MET cc_start: 0.8928 (tpt) cc_final: 0.8693 (tpp) REVERT: 7 459 MET cc_start: 0.9319 (ppp) cc_final: 0.8971 (ppp) REVERT: A 100 MET cc_start: 0.8452 (tmm) cc_final: 0.8228 (tmm) REVERT: D 129 MET cc_start: 0.8742 (mpp) cc_final: 0.8328 (mpp) REVERT: G 774 MET cc_start: 0.9159 (tpt) cc_final: 0.8861 (tpt) REVERT: H 774 MET cc_start: 0.6747 (ptt) cc_final: 0.6070 (ptt) REVERT: M 1470 MET cc_start: 0.6933 (mpp) cc_final: 0.6497 (mpp) REVERT: M 1482 MET cc_start: 0.7307 (tpt) cc_final: 0.6958 (tpt) REVERT: M 1794 MET cc_start: 0.8480 (tmm) cc_final: 0.8146 (tmm) REVERT: N 217 MET cc_start: 0.9249 (ptm) cc_final: 0.8862 (ptm) REVERT: N 639 MET cc_start: 0.8220 (mmp) cc_final: 0.7819 (mmm) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.5626 time to fit residues: 195.1727 Evaluate side-chains 183 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 5.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 398 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 597 optimal weight: 8.9990 chunk 488 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 718 optimal weight: 6.9990 chunk 776 optimal weight: 8.9990 chunk 640 optimal weight: 5.9990 chunk 712 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 576 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 GLN ** 2 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 760 GLN ** 3 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 652 GLN ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 258 GLN ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 514 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 130 ASN E 133 ASN E 141 GLN E 225 GLN E 229 GLN E 296 GLN E 342 ASN F 555 GLN ** F 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 843 ASN F 916 ASN H 565 ASN H 843 ASN M1806 ASN M2001 ASN N 48 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 65048 Z= 0.370 Angle : 0.700 10.627 88136 Z= 0.363 Chirality : 0.043 0.186 10066 Planarity : 0.005 0.064 11194 Dihedral : 8.697 147.873 8948 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % 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 (0.10), residues: 7818 helix: 1.20 (0.09), residues: 3237 sheet: -1.41 (0.14), residues: 1330 loop : -1.00 (0.11), residues: 3251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP N 491 HIS 0.013 0.002 HIS G 629 PHE 0.037 0.002 PHE F 766 TYR 0.053 0.002 TYR F 651 ARG 0.040 0.001 ARG F 649 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 6.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 306 MET cc_start: 0.9155 (tpp) cc_final: 0.8859 (tpp) REVERT: 3 386 MET cc_start: 0.8611 (ppp) cc_final: 0.8273 (ppp) REVERT: 3 407 MET cc_start: 0.8657 (ppp) cc_final: 0.8385 (ppp) REVERT: 4 272 MET cc_start: 0.9686 (mmm) cc_final: 0.9244 (tmm) REVERT: 4 280 MET cc_start: 0.8820 (mmm) cc_final: 0.8382 (tpt) REVERT: 4 780 MET cc_start: 0.8211 (ppp) cc_final: 0.7887 (ppp) REVERT: 4 847 MET cc_start: 0.8027 (mpp) cc_final: 0.7728 (mpp) REVERT: 4 881 MET cc_start: 0.6208 (pmm) cc_final: 0.5926 (ptp) REVERT: 5 270 MET cc_start: 0.8690 (ppp) cc_final: 0.8459 (ppp) REVERT: 6 373 MET cc_start: 0.9123 (tpp) cc_final: 0.8819 (tpp) REVERT: 6 629 MET cc_start: 0.9190 (mmp) cc_final: 0.8610 (mmm) REVERT: 6 656 MET cc_start: 0.9640 (ptm) cc_final: 0.9305 (ptm) REVERT: 6 803 MET cc_start: 0.9534 (mtm) cc_final: 0.9040 (mtt) REVERT: 7 66 MET cc_start: 0.9410 (mmp) cc_final: 0.9022 (mmp) REVERT: 7 125 MET cc_start: 0.8932 (tpt) cc_final: 0.8683 (tpt) REVERT: 7 459 MET cc_start: 0.9422 (ppp) cc_final: 0.8977 (ppp) REVERT: A 100 MET cc_start: 0.8614 (tmm) cc_final: 0.8360 (tmm) REVERT: B 1 MET cc_start: 0.8034 (tmm) cc_final: 0.7814 (tmm) REVERT: D 129 MET cc_start: 0.8732 (mpp) cc_final: 0.8400 (mpp) REVERT: H 774 MET cc_start: 0.7094 (ptt) cc_final: 0.6527 (ptt) REVERT: M 1452 MET cc_start: 0.5302 (tpt) cc_final: 0.4541 (pmm) REVERT: M 1470 MET cc_start: 0.6647 (mpp) cc_final: 0.6291 (mpp) REVERT: M 1482 MET cc_start: 0.7929 (tpt) cc_final: 0.7645 (tpt) REVERT: M 1794 MET cc_start: 0.8483 (tmm) cc_final: 0.8146 (tmm) REVERT: N 217 MET cc_start: 0.9343 (ptm) cc_final: 0.8927 (ptm) REVERT: N 266 MET cc_start: 0.4723 (ppp) cc_final: 0.4445 (ppp) REVERT: N 414 MET cc_start: 0.8846 (mpp) cc_final: 0.8485 (mpp) REVERT: N 494 MET cc_start: 0.9238 (mtt) cc_final: 0.8767 (tpp) REVERT: N 639 MET cc_start: 0.8330 (mmp) cc_final: 0.7889 (mmm) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.5729 time to fit residues: 195.6494 Evaluate side-chains 183 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 5.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 710 optimal weight: 1.9990 chunk 540 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 342 optimal weight: 20.0000 chunk 482 optimal weight: 1.9990 chunk 721 optimal weight: 7.9990 chunk 763 optimal weight: 8.9990 chunk 376 optimal weight: 5.9990 chunk 683 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 290 HIS 3 691 ASN ** 4 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 584 GLN ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 506 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN F 553 GLN F 741 HIS F 816 GLN F 843 ASN F 887 HIS ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 915 ASN H 843 ASN ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1806 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 666 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 65048 Z= 0.179 Angle : 0.538 8.650 88136 Z= 0.282 Chirality : 0.041 0.250 10066 Planarity : 0.004 0.079 11194 Dihedral : 8.493 146.701 8948 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.31 % 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: 0.05 (0.10), residues: 7818 helix: 1.55 (0.09), residues: 3223 sheet: -1.25 (0.14), residues: 1320 loop : -0.91 (0.11), residues: 3275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP N 491 HIS 0.007 0.001 HIS F 634 PHE 0.032 0.001 PHE F 766 TYR 0.034 0.001 TYR E 2 ARG 0.006 0.000 ARG 3 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 9.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.8404 (tmm) cc_final: 0.7858 (tmm) REVERT: 2 783 MET cc_start: 0.8780 (pmm) cc_final: 0.8562 (ttp) REVERT: 3 261 MET cc_start: 0.9099 (mmp) cc_final: 0.7952 (mmp) REVERT: 3 306 MET cc_start: 0.9117 (tpp) cc_final: 0.8814 (tpp) REVERT: 3 386 MET cc_start: 0.8638 (ppp) cc_final: 0.8334 (ppp) REVERT: 3 407 MET cc_start: 0.8728 (ppp) cc_final: 0.8435 (ppp) REVERT: 4 272 MET cc_start: 0.9677 (mmm) cc_final: 0.9436 (tpp) REVERT: 4 280 MET cc_start: 0.8793 (mmm) cc_final: 0.8530 (mtp) REVERT: 4 780 MET cc_start: 0.8055 (ppp) cc_final: 0.7751 (ppp) REVERT: 4 847 MET cc_start: 0.8083 (mpp) cc_final: 0.7770 (mpp) REVERT: 6 373 MET cc_start: 0.9170 (tpp) cc_final: 0.8730 (tpp) REVERT: 6 629 MET cc_start: 0.9202 (mmp) cc_final: 0.8687 (mmm) REVERT: 6 656 MET cc_start: 0.9612 (ptm) cc_final: 0.9213 (ptm) REVERT: 6 803 MET cc_start: 0.9528 (mtm) cc_final: 0.8993 (mtt) REVERT: 7 66 MET cc_start: 0.9342 (mmp) cc_final: 0.9133 (mmp) REVERT: 7 125 MET cc_start: 0.8887 (tpt) cc_final: 0.8685 (tpp) REVERT: 7 402 MET cc_start: 0.9655 (tpt) cc_final: 0.9408 (mmt) REVERT: 7 459 MET cc_start: 0.9387 (ppp) cc_final: 0.8905 (ppp) REVERT: A 1 MET cc_start: 0.8547 (tpp) cc_final: 0.7551 (tpp) REVERT: A 100 MET cc_start: 0.8552 (tmm) cc_final: 0.8271 (tmm) REVERT: D 129 MET cc_start: 0.8625 (mpp) cc_final: 0.8268 (mpp) REVERT: H 774 MET cc_start: 0.7068 (ptt) cc_final: 0.6528 (ptt) REVERT: M 1366 MET cc_start: 0.7584 (mmm) cc_final: 0.7122 (mmm) REVERT: M 1452 MET cc_start: 0.5311 (tpt) cc_final: 0.4595 (pmm) REVERT: M 1470 MET cc_start: 0.6644 (mpp) cc_final: 0.6363 (mpp) REVERT: M 1482 MET cc_start: 0.7646 (tpt) cc_final: 0.7256 (tpp) REVERT: M 1794 MET cc_start: 0.8490 (tmm) cc_final: 0.8136 (tmm) REVERT: N 217 MET cc_start: 0.9248 (ptm) cc_final: 0.8859 (ptm) REVERT: N 414 MET cc_start: 0.8878 (mpp) cc_final: 0.8478 (mpp) REVERT: N 494 MET cc_start: 0.9267 (mtt) cc_final: 0.8952 (tpt) REVERT: N 639 MET cc_start: 0.8367 (mmp) cc_final: 0.7942 (mmm) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.5771 time to fit residues: 202.2173 Evaluate side-chains 185 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 635 optimal weight: 9.9990 chunk 433 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 568 optimal weight: 0.9990 chunk 315 optimal weight: 6.9990 chunk 651 optimal weight: 8.9990 chunk 527 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 389 optimal weight: 10.0000 chunk 685 optimal weight: 9.9990 chunk 192 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 366 ASN ** 4 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 871 ASN ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 550 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN A 188 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** F 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 843 ASN H 843 ASN M1806 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 65048 Z= 0.310 Angle : 0.613 8.796 88136 Z= 0.319 Chirality : 0.041 0.190 10066 Planarity : 0.004 0.063 11194 Dihedral : 8.555 147.054 8948 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.03 % Allowed : 2.52 % Favored : 97.45 % 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: -0.11 (0.10), residues: 7818 helix: 1.42 (0.09), residues: 3249 sheet: -1.38 (0.14), residues: 1334 loop : -0.98 (0.11), residues: 3235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 3 153 HIS 0.008 0.001 HIS M1352 PHE 0.034 0.002 PHE F 766 TYR 0.034 0.002 TYR E 121 ARG 0.009 0.000 ARG 3 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 5.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 823 MET cc_start: 0.9107 (ptp) cc_final: 0.8883 (ptp) REVERT: 3 306 MET cc_start: 0.9075 (tpp) cc_final: 0.8788 (tpp) REVERT: 3 407 MET cc_start: 0.8659 (ppp) cc_final: 0.8350 (ppp) REVERT: 4 272 MET cc_start: 0.9679 (mmm) cc_final: 0.9425 (tpp) REVERT: 4 280 MET cc_start: 0.8787 (mmm) cc_final: 0.8565 (mtp) REVERT: 4 382 MET cc_start: 0.8442 (mpp) cc_final: 0.8201 (mpp) REVERT: 4 780 MET cc_start: 0.8286 (ppp) cc_final: 0.7945 (ppp) REVERT: 4 801 MET cc_start: 0.9391 (ptp) cc_final: 0.9188 (ptt) REVERT: 4 847 MET cc_start: 0.8017 (mpp) cc_final: 0.7729 (mpp) REVERT: 4 881 MET cc_start: 0.6373 (ptt) cc_final: 0.5260 (pmm) REVERT: 6 373 MET cc_start: 0.9193 (tpp) cc_final: 0.8904 (tpp) REVERT: 6 629 MET cc_start: 0.9267 (mmp) cc_final: 0.8790 (mmm) REVERT: 6 656 MET cc_start: 0.9622 (ptm) cc_final: 0.9282 (ptm) REVERT: 6 803 MET cc_start: 0.9498 (mtm) cc_final: 0.8885 (mtt) REVERT: 7 66 MET cc_start: 0.9348 (mmp) cc_final: 0.9067 (mmp) REVERT: 7 459 MET cc_start: 0.9259 (ppp) cc_final: 0.8957 (ppp) REVERT: A 1 MET cc_start: 0.8904 (tpp) cc_final: 0.7725 (tpp) REVERT: A 100 MET cc_start: 0.8646 (tmm) cc_final: 0.8365 (tmm) REVERT: B 189 MET cc_start: 0.8690 (tpp) cc_final: 0.8211 (tpp) REVERT: D 129 MET cc_start: 0.8681 (mpp) cc_final: 0.8247 (mpp) REVERT: F 659 MET cc_start: 0.7897 (tpt) cc_final: 0.7589 (tpp) REVERT: H 774 MET cc_start: 0.7064 (ptt) cc_final: 0.6633 (ptt) REVERT: M 1452 MET cc_start: 0.5320 (tpt) cc_final: 0.4671 (pmm) REVERT: M 1465 MET cc_start: 0.7412 (ppp) cc_final: 0.7207 (ppp) REVERT: M 1470 MET cc_start: 0.6370 (mpp) cc_final: 0.6152 (mpp) REVERT: N 217 MET cc_start: 0.9323 (ptm) cc_final: 0.8923 (ptm) REVERT: N 414 MET cc_start: 0.8808 (mpp) cc_final: 0.8470 (mpp) REVERT: N 639 MET cc_start: 0.8387 (mmp) cc_final: 0.7934 (mmm) outliers start: 2 outliers final: 2 residues processed: 191 average time/residue: 0.5712 time to fit residues: 197.7131 Evaluate side-chains 186 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 5.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 256 optimal weight: 2.9990 chunk 687 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 448 optimal weight: 0.7980 chunk 188 optimal weight: 30.0000 chunk 764 optimal weight: 20.0000 chunk 634 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 401 optimal weight: 8.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 366 ASN 2 780 GLN 3 253 HIS 3 532 ASN ** 4 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 379 GLN ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** F 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 843 ASN H 843 ASN M1806 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 65048 Z= 0.272 Angle : 0.591 8.965 88136 Z= 0.309 Chirality : 0.041 0.238 10066 Planarity : 0.004 0.064 11194 Dihedral : 8.477 146.930 8948 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.10), residues: 7818 helix: 1.39 (0.09), residues: 3254 sheet: -1.42 (0.14), residues: 1361 loop : -0.98 (0.11), residues: 3203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 3 153 HIS 0.007 0.001 HIS F 634 PHE 0.034 0.002 PHE F 766 TYR 0.031 0.002 TYR F 862 ARG 0.011 0.000 ARG 7 673 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 5.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 261 MET cc_start: 0.9080 (mmp) cc_final: 0.7862 (mmp) REVERT: 3 306 MET cc_start: 0.9083 (tpp) cc_final: 0.8796 (tpp) REVERT: 3 407 MET cc_start: 0.8678 (ppp) cc_final: 0.8447 (ppp) REVERT: 4 272 MET cc_start: 0.9677 (mmm) cc_final: 0.9425 (tpp) REVERT: 4 280 MET cc_start: 0.8794 (mmm) cc_final: 0.8563 (mtp) REVERT: 4 780 MET cc_start: 0.8275 (ppp) cc_final: 0.7966 (ppp) REVERT: 4 801 MET cc_start: 0.9383 (ptp) cc_final: 0.9099 (ptt) REVERT: 4 847 MET cc_start: 0.8071 (mpp) cc_final: 0.7786 (mpp) REVERT: 5 276 MET cc_start: 0.9217 (pmm) cc_final: 0.8794 (pmm) REVERT: 6 629 MET cc_start: 0.9221 (mmp) cc_final: 0.8808 (mmm) REVERT: 6 656 MET cc_start: 0.9614 (ptm) cc_final: 0.9278 (ptm) REVERT: 6 803 MET cc_start: 0.9491 (mtm) cc_final: 0.8850 (mtt) REVERT: 7 66 MET cc_start: 0.9333 (mmp) cc_final: 0.9042 (mmp) REVERT: 7 459 MET cc_start: 0.9250 (ppp) cc_final: 0.8844 (ppp) REVERT: A 1 MET cc_start: 0.8867 (tpp) cc_final: 0.7616 (tpp) REVERT: B 189 MET cc_start: 0.8673 (tpp) cc_final: 0.8289 (tpp) REVERT: D 129 MET cc_start: 0.8659 (mpp) cc_final: 0.8222 (mpp) REVERT: F 659 MET cc_start: 0.7886 (tpt) cc_final: 0.7624 (tpp) REVERT: H 774 MET cc_start: 0.7156 (ptt) cc_final: 0.6750 (ptt) REVERT: M 1366 MET cc_start: 0.7959 (mmm) cc_final: 0.7508 (mmm) REVERT: M 1452 MET cc_start: 0.5311 (tpt) cc_final: 0.4657 (pmm) REVERT: M 1465 MET cc_start: 0.7555 (ppp) cc_final: 0.7315 (ppp) REVERT: M 1470 MET cc_start: 0.6419 (mpp) cc_final: 0.6116 (mpp) REVERT: M 1794 MET cc_start: 0.8721 (tmm) cc_final: 0.8461 (tmm) REVERT: M 2062 MET cc_start: 0.8893 (ppp) cc_final: 0.8621 (ppp) REVERT: N 217 MET cc_start: 0.9357 (ptm) cc_final: 0.8934 (ptm) REVERT: N 414 MET cc_start: 0.8855 (mpp) cc_final: 0.8523 (mpp) REVERT: N 494 MET cc_start: 0.8922 (tpt) cc_final: 0.8721 (tpp) REVERT: N 639 MET cc_start: 0.8405 (mmp) cc_final: 0.7958 (mmm) REVERT: N 673 MET cc_start: 0.8057 (mmp) cc_final: 0.7268 (tpp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.5747 time to fit residues: 193.6728 Evaluate side-chains 184 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 736 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 435 optimal weight: 5.9990 chunk 558 optimal weight: 20.0000 chunk 432 optimal weight: 0.9980 chunk 643 optimal weight: 10.0000 chunk 426 optimal weight: 0.0870 chunk 761 optimal weight: 8.9990 chunk 476 optimal weight: 5.9990 chunk 464 optimal weight: 0.9980 chunk 351 optimal weight: 7.9990 overall best weight: 2.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 366 ASN 2 391 GLN 2 653 ASN ** 4 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 HIS F 843 ASN G 634 HIS ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 702 ASN H 725 ASN H 843 ASN M1806 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 65048 Z= 0.178 Angle : 0.540 9.168 88136 Z= 0.282 Chirality : 0.041 0.183 10066 Planarity : 0.004 0.065 11194 Dihedral : 8.356 146.062 8948 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: 0.08 (0.10), residues: 7818 helix: 1.61 (0.09), residues: 3235 sheet: -1.26 (0.14), residues: 1346 loop : -0.91 (0.11), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 3 111 HIS 0.006 0.001 HIS F 634 PHE 0.029 0.001 PHE F 766 TYR 0.029 0.001 TYR F 862 ARG 0.006 0.000 ARG 2 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.8262 (ttm) cc_final: 0.7964 (tpp) REVERT: 3 136 MET cc_start: 0.8012 (tmm) cc_final: 0.7616 (tmm) REVERT: 3 261 MET cc_start: 0.9090 (mmp) cc_final: 0.7890 (mmp) REVERT: 3 306 MET cc_start: 0.9067 (tpp) cc_final: 0.8803 (tpp) REVERT: 3 407 MET cc_start: 0.8659 (ppp) cc_final: 0.8405 (ppp) REVERT: 4 272 MET cc_start: 0.9665 (mmm) cc_final: 0.9399 (tpp) REVERT: 4 280 MET cc_start: 0.8803 (mmm) cc_final: 0.8508 (mtp) REVERT: 4 780 MET cc_start: 0.8180 (ppp) cc_final: 0.7902 (ppp) REVERT: 4 801 MET cc_start: 0.9319 (ptp) cc_final: 0.9012 (ptp) REVERT: 4 847 MET cc_start: 0.8085 (mpp) cc_final: 0.7768 (mpp) REVERT: 4 881 MET cc_start: 0.6286 (ptm) cc_final: 0.4742 (pmm) REVERT: 5 276 MET cc_start: 0.9173 (pmm) cc_final: 0.8772 (pmm) REVERT: 6 373 MET cc_start: 0.9255 (tpp) cc_final: 0.8841 (tpp) REVERT: 6 629 MET cc_start: 0.9227 (mmp) cc_final: 0.8836 (mmm) REVERT: 6 656 MET cc_start: 0.9601 (ptm) cc_final: 0.9229 (ptm) REVERT: 6 803 MET cc_start: 0.9489 (mtm) cc_final: 0.8835 (mtt) REVERT: 7 66 MET cc_start: 0.9315 (mmp) cc_final: 0.9025 (mmp) REVERT: 7 459 MET cc_start: 0.9285 (ppp) cc_final: 0.8835 (ppp) REVERT: A 1 MET cc_start: 0.8910 (tpp) cc_final: 0.8516 (tpp) REVERT: B 189 MET cc_start: 0.8529 (tpp) cc_final: 0.8073 (tpp) REVERT: D 129 MET cc_start: 0.8572 (mpp) cc_final: 0.8203 (mpp) REVERT: H 774 MET cc_start: 0.7088 (ptt) cc_final: 0.6685 (ptt) REVERT: H 778 MET cc_start: 0.7441 (pmm) cc_final: 0.7037 (pmm) REVERT: M 1366 MET cc_start: 0.7817 (mmm) cc_final: 0.7347 (mmm) REVERT: M 1452 MET cc_start: 0.5311 (tpt) cc_final: 0.4668 (pmm) REVERT: M 1465 MET cc_start: 0.7563 (ppp) cc_final: 0.7320 (ppp) REVERT: M 1470 MET cc_start: 0.6393 (mpp) cc_final: 0.6100 (mpp) REVERT: M 1794 MET cc_start: 0.8681 (tmm) cc_final: 0.8375 (tmm) REVERT: M 1958 MET cc_start: 0.9202 (mpp) cc_final: 0.8773 (mpp) REVERT: M 2062 MET cc_start: 0.8868 (ppp) cc_final: 0.8572 (ppp) REVERT: N 217 MET cc_start: 0.9339 (ptm) cc_final: 0.8894 (ptm) REVERT: N 639 MET cc_start: 0.8546 (mmp) cc_final: 0.8102 (mmm) REVERT: N 673 MET cc_start: 0.7777 (mmp) cc_final: 0.7082 (tpp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.5887 time to fit residues: 200.5274 Evaluate side-chains 184 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 471 optimal weight: 6.9990 chunk 304 optimal weight: 0.4980 chunk 454 optimal weight: 0.8980 chunk 229 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 484 optimal weight: 1.9990 chunk 518 optimal weight: 2.9990 chunk 376 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 598 optimal weight: 0.0970 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 175 HIS ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 620 HIS A 206 GLN E 7 GLN ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 843 ASN G 573 GLN G 665 ASN H 843 ASN ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1806 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 65048 Z= 0.147 Angle : 0.524 11.539 88136 Z= 0.273 Chirality : 0.041 0.180 10066 Planarity : 0.004 0.120 11194 Dihedral : 8.232 145.059 8948 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.01 % Allowed : 0.77 % Favored : 99.22 % 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: 0.22 (0.10), residues: 7818 helix: 1.72 (0.09), residues: 3234 sheet: -1.15 (0.14), residues: 1348 loop : -0.85 (0.11), residues: 3236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M1505 HIS 0.005 0.001 HIS F 634 PHE 0.026 0.001 PHE F 766 TYR 0.025 0.001 TYR F 862 ARG 0.011 0.000 ARG E 590 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 6.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 823 MET cc_start: 0.9092 (ptp) cc_final: 0.8891 (ptp) REVERT: 3 136 MET cc_start: 0.8040 (tmm) cc_final: 0.7670 (tmm) REVERT: 3 261 MET cc_start: 0.9115 (mmp) cc_final: 0.7967 (mmp) REVERT: 3 306 MET cc_start: 0.9063 (tpp) cc_final: 0.8772 (tpp) REVERT: 3 407 MET cc_start: 0.8616 (ppp) cc_final: 0.8325 (ppp) REVERT: 3 490 MET cc_start: 0.9101 (ptt) cc_final: 0.8744 (ttp) REVERT: 4 272 MET cc_start: 0.9656 (mmm) cc_final: 0.9392 (tpp) REVERT: 4 280 MET cc_start: 0.8800 (mmm) cc_final: 0.8509 (mtp) REVERT: 4 649 MET cc_start: 0.9040 (ppp) cc_final: 0.8681 (ppp) REVERT: 4 780 MET cc_start: 0.8167 (ppp) cc_final: 0.7890 (ppp) REVERT: 4 811 MET cc_start: 0.8900 (ppp) cc_final: 0.8700 (ppp) REVERT: 4 847 MET cc_start: 0.8103 (mpp) cc_final: 0.7791 (mpp) REVERT: 4 881 MET cc_start: 0.6029 (ptm) cc_final: 0.3909 (pmm) REVERT: 5 276 MET cc_start: 0.9166 (pmm) cc_final: 0.8755 (pmm) REVERT: 6 373 MET cc_start: 0.9252 (tpp) cc_final: 0.8830 (tpp) REVERT: 6 629 MET cc_start: 0.9224 (mmp) cc_final: 0.8866 (mmm) REVERT: 6 656 MET cc_start: 0.9604 (ptm) cc_final: 0.9223 (ptm) REVERT: 6 803 MET cc_start: 0.9484 (mtm) cc_final: 0.8818 (mtt) REVERT: 7 66 MET cc_start: 0.9311 (mmp) cc_final: 0.9021 (mmp) REVERT: 7 402 MET cc_start: 0.9634 (tmm) cc_final: 0.9234 (mmt) REVERT: 7 459 MET cc_start: 0.9319 (ppp) cc_final: 0.8861 (ppp) REVERT: A 1 MET cc_start: 0.8877 (tpp) cc_final: 0.8189 (tpp) REVERT: A 100 MET cc_start: 0.8328 (tpt) cc_final: 0.8047 (tpt) REVERT: B 189 MET cc_start: 0.8576 (tpp) cc_final: 0.8144 (tpp) REVERT: D 129 MET cc_start: 0.8673 (mpp) cc_final: 0.8350 (mpp) REVERT: H 659 MET cc_start: 0.6672 (tmm) cc_final: 0.6247 (tmm) REVERT: H 774 MET cc_start: 0.7010 (ptt) cc_final: 0.6639 (ptt) REVERT: H 778 MET cc_start: 0.7476 (pmm) cc_final: 0.7052 (pmm) REVERT: M 1359 MET cc_start: 0.2514 (tpt) cc_final: 0.2248 (mmm) REVERT: M 1366 MET cc_start: 0.7892 (mmm) cc_final: 0.7431 (mmm) REVERT: M 1452 MET cc_start: 0.5288 (tpt) cc_final: 0.4755 (pmm) REVERT: M 1465 MET cc_start: 0.7532 (ppp) cc_final: 0.7303 (ppp) REVERT: M 1470 MET cc_start: 0.6437 (mpp) cc_final: 0.6146 (mpp) REVERT: M 1794 MET cc_start: 0.8732 (tmm) cc_final: 0.8415 (tmm) REVERT: M 2062 MET cc_start: 0.8938 (ppp) cc_final: 0.8459 (ppp) REVERT: N 217 MET cc_start: 0.9321 (ptm) cc_final: 0.8877 (ptm) REVERT: N 639 MET cc_start: 0.8652 (mmp) cc_final: 0.8270 (mmm) REVERT: N 673 MET cc_start: 0.7742 (mmp) cc_final: 0.6941 (tpp) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.5750 time to fit residues: 198.2824 Evaluate side-chains 184 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 5.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 692 optimal weight: 6.9990 chunk 729 optimal weight: 0.9980 chunk 665 optimal weight: 9.9990 chunk 709 optimal weight: 5.9990 chunk 427 optimal weight: 6.9990 chunk 309 optimal weight: 20.0000 chunk 557 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 641 optimal weight: 0.4980 chunk 671 optimal weight: 10.0000 chunk 707 optimal weight: 2.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 344 ASN ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN F 843 ASN H 843 ASN ** H 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1806 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 65048 Z= 0.161 Angle : 0.525 8.955 88136 Z= 0.273 Chirality : 0.040 0.179 10066 Planarity : 0.004 0.077 11194 Dihedral : 8.181 144.818 8948 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.10), residues: 7818 helix: 1.76 (0.09), residues: 3234 sheet: -1.11 (0.14), residues: 1359 loop : -0.80 (0.11), residues: 3225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 491 HIS 0.005 0.001 HIS F 634 PHE 0.032 0.001 PHE N 462 TYR 0.021 0.001 TYR G 862 ARG 0.005 0.000 ARG 3 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 5.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 783 MET cc_start: 0.9271 (mpp) cc_final: 0.8617 (ttm) REVERT: 3 136 MET cc_start: 0.8050 (tmm) cc_final: 0.7668 (tmm) REVERT: 3 261 MET cc_start: 0.9111 (mmp) cc_final: 0.8024 (mmp) REVERT: 3 306 MET cc_start: 0.9055 (tpp) cc_final: 0.8778 (tpp) REVERT: 3 386 MET cc_start: 0.8631 (ppp) cc_final: 0.8383 (ppp) REVERT: 3 407 MET cc_start: 0.8646 (ppp) cc_final: 0.8357 (ppp) REVERT: 4 272 MET cc_start: 0.9652 (mmm) cc_final: 0.9395 (tpp) REVERT: 4 280 MET cc_start: 0.8802 (mmm) cc_final: 0.8505 (mtp) REVERT: 4 382 MET cc_start: 0.8582 (mpp) cc_final: 0.8235 (mpp) REVERT: 4 649 MET cc_start: 0.9080 (ppp) cc_final: 0.8707 (ppp) REVERT: 4 780 MET cc_start: 0.8156 (ppp) cc_final: 0.7861 (ppp) REVERT: 4 847 MET cc_start: 0.8057 (mpp) cc_final: 0.7750 (mpp) REVERT: 4 881 MET cc_start: 0.5891 (ptm) cc_final: 0.4037 (pmm) REVERT: 5 276 MET cc_start: 0.9203 (pmm) cc_final: 0.8782 (pmm) REVERT: 6 373 MET cc_start: 0.9242 (tpp) cc_final: 0.8815 (tpp) REVERT: 6 629 MET cc_start: 0.9254 (mmp) cc_final: 0.8905 (mmm) REVERT: 6 656 MET cc_start: 0.9615 (ptm) cc_final: 0.9256 (ptm) REVERT: 6 803 MET cc_start: 0.9471 (mtm) cc_final: 0.8788 (mtt) REVERT: 7 66 MET cc_start: 0.9317 (mmp) cc_final: 0.9028 (mmp) REVERT: 7 459 MET cc_start: 0.9355 (ppp) cc_final: 0.8687 (ppp) REVERT: A 1 MET cc_start: 0.8921 (tpp) cc_final: 0.8518 (tpp) REVERT: B 189 MET cc_start: 0.8588 (tpp) cc_final: 0.8199 (tpp) REVERT: D 129 MET cc_start: 0.8709 (mpp) cc_final: 0.8387 (mpp) REVERT: H 659 MET cc_start: 0.6736 (tmm) cc_final: 0.6437 (tmm) REVERT: H 774 MET cc_start: 0.7075 (ptt) cc_final: 0.6720 (ptt) REVERT: H 778 MET cc_start: 0.7385 (pmm) cc_final: 0.6947 (pmm) REVERT: H 847 MET cc_start: 0.5728 (pmm) cc_final: 0.5236 (pmm) REVERT: M 1359 MET cc_start: 0.2545 (tpt) cc_final: 0.2297 (mmm) REVERT: M 1366 MET cc_start: 0.7921 (mmm) cc_final: 0.7445 (mmm) REVERT: M 1452 MET cc_start: 0.5249 (tpt) cc_final: 0.4828 (pmm) REVERT: M 1465 MET cc_start: 0.7532 (ppp) cc_final: 0.7327 (ppp) REVERT: M 1470 MET cc_start: 0.6415 (mpp) cc_final: 0.6108 (mpp) REVERT: M 1794 MET cc_start: 0.8751 (tmm) cc_final: 0.8405 (tmm) REVERT: M 2062 MET cc_start: 0.8928 (ppp) cc_final: 0.8603 (ppp) REVERT: N 217 MET cc_start: 0.9311 (ptm) cc_final: 0.8870 (ptm) REVERT: N 414 MET cc_start: 0.8866 (mpp) cc_final: 0.8635 (mpp) REVERT: N 494 MET cc_start: 0.9087 (mpp) cc_final: 0.8472 (tpt) REVERT: N 639 MET cc_start: 0.8688 (mmp) cc_final: 0.8317 (mmm) REVERT: N 673 MET cc_start: 0.7810 (mmp) cc_final: 0.6956 (tpp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.5781 time to fit residues: 196.3964 Evaluate side-chains 184 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 5.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 465 optimal weight: 4.9990 chunk 750 optimal weight: 8.9990 chunk 457 optimal weight: 6.9990 chunk 355 optimal weight: 20.0000 chunk 521 optimal weight: 0.7980 chunk 787 optimal weight: 1.9990 chunk 724 optimal weight: 0.2980 chunk 626 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 484 optimal weight: 0.0270 chunk 384 optimal weight: 7.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 GLN ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN F 843 ASN H 843 ASN ** H 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1806 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 65048 Z= 0.147 Angle : 0.516 9.154 88136 Z= 0.268 Chirality : 0.040 0.215 10066 Planarity : 0.004 0.066 11194 Dihedral : 8.134 144.571 8948 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 0.34 (0.10), residues: 7818 helix: 1.80 (0.09), residues: 3235 sheet: -1.02 (0.14), residues: 1346 loop : -0.79 (0.11), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 3 111 HIS 0.004 0.001 HIS 7 538 PHE 0.024 0.001 PHE F 766 TYR 0.019 0.001 TYR H 862 ARG 0.005 0.000 ARG 2 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15636 Ramachandran restraints generated. 7818 Oldfield, 0 Emsley, 7818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 5.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 136 MET cc_start: 0.8046 (tmm) cc_final: 0.7660 (tmm) REVERT: 3 261 MET cc_start: 0.9127 (mmp) cc_final: 0.8086 (mmp) REVERT: 3 306 MET cc_start: 0.9076 (tpp) cc_final: 0.8790 (tpp) REVERT: 3 407 MET cc_start: 0.8664 (ppp) cc_final: 0.8364 (ppp) REVERT: 4 272 MET cc_start: 0.9649 (mmm) cc_final: 0.9360 (tmm) REVERT: 4 280 MET cc_start: 0.8808 (mmm) cc_final: 0.8429 (mtp) REVERT: 4 649 MET cc_start: 0.9121 (ppp) cc_final: 0.8772 (ppp) REVERT: 4 780 MET cc_start: 0.8175 (ppp) cc_final: 0.7877 (ppp) REVERT: 4 847 MET cc_start: 0.8052 (mpp) cc_final: 0.7747 (mpp) REVERT: 4 881 MET cc_start: 0.5908 (ptm) cc_final: 0.4098 (pmm) REVERT: 5 276 MET cc_start: 0.9193 (pmm) cc_final: 0.8769 (pmm) REVERT: 6 373 MET cc_start: 0.9237 (tpp) cc_final: 0.8827 (tpp) REVERT: 6 629 MET cc_start: 0.9242 (mmp) cc_final: 0.8896 (mmm) REVERT: 6 656 MET cc_start: 0.9602 (ptm) cc_final: 0.9234 (ptm) REVERT: 6 803 MET cc_start: 0.9474 (mtm) cc_final: 0.8974 (mtt) REVERT: 7 66 MET cc_start: 0.9324 (mmp) cc_final: 0.9043 (mmp) REVERT: 7 459 MET cc_start: 0.9353 (ppp) cc_final: 0.8675 (ppp) REVERT: A 1 MET cc_start: 0.8870 (tpp) cc_final: 0.8458 (tpp) REVERT: B 189 MET cc_start: 0.8573 (tpp) cc_final: 0.8178 (tpp) REVERT: D 129 MET cc_start: 0.8703 (mpp) cc_final: 0.8377 (mpp) REVERT: H 774 MET cc_start: 0.7088 (ptt) cc_final: 0.6747 (ptt) REVERT: H 778 MET cc_start: 0.7405 (pmm) cc_final: 0.6967 (pmm) REVERT: H 847 MET cc_start: 0.6021 (pmm) cc_final: 0.5449 (pmm) REVERT: M 1359 MET cc_start: 0.2416 (tpt) cc_final: 0.2183 (mmm) REVERT: M 1366 MET cc_start: 0.7921 (mmm) cc_final: 0.7471 (mmm) REVERT: M 1452 MET cc_start: 0.5288 (tpt) cc_final: 0.4895 (pmm) REVERT: M 1465 MET cc_start: 0.7521 (ppp) cc_final: 0.7310 (ppp) REVERT: M 1470 MET cc_start: 0.6413 (mpp) cc_final: 0.6105 (mpp) REVERT: M 1482 MET cc_start: 0.7778 (tpt) cc_final: 0.7520 (tpt) REVERT: M 1794 MET cc_start: 0.8739 (tmm) cc_final: 0.8413 (tmm) REVERT: M 1958 MET cc_start: 0.9265 (mpp) cc_final: 0.8899 (mpp) REVERT: M 2062 MET cc_start: 0.8936 (ppp) cc_final: 0.8601 (ppp) REVERT: N 217 MET cc_start: 0.9303 (ptm) cc_final: 0.8853 (ptm) REVERT: N 414 MET cc_start: 0.8860 (mpp) cc_final: 0.8641 (mpp) REVERT: N 494 MET cc_start: 0.9176 (mpp) cc_final: 0.8250 (tpt) REVERT: N 639 MET cc_start: 0.8687 (mmp) cc_final: 0.8305 (mmm) REVERT: N 673 MET cc_start: 0.7783 (mmp) cc_final: 0.6887 (tpp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.5958 time to fit residues: 201.0731 Evaluate side-chains 184 residues out of total 7128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 5.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 790 random chunks: chunk 497 optimal weight: 4.9990 chunk 667 optimal weight: 50.0000 chunk 191 optimal weight: 30.0000 chunk 577 optimal weight: 20.0000 chunk 92 optimal weight: 0.0370 chunk 174 optimal weight: 1.9990 chunk 627 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 644 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 258 GLN ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN F 843 ASN H 843 ASN ** H 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1806 ASN N 13 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.028743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.022557 restraints weight = 1216210.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.023171 restraints weight = 801335.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.023635 restraints weight = 503293.314| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 65048 Z= 0.184 Angle : 0.534 9.021 88136 Z= 0.277 Chirality : 0.040 0.212 10066 Planarity : 0.004 0.066 11194 Dihedral : 8.138 144.831 8948 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.10), residues: 7818 helix: 1.83 (0.09), residues: 3230 sheet: -1.04 (0.14), residues: 1368 loop : -0.78 (0.11), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 491 HIS 0.005 0.001 HIS F 634 PHE 0.037 0.001 PHE M1953 TYR 0.018 0.001 TYR H 862 ARG 0.004 0.000 ARG 3 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7504.72 seconds wall clock time: 139 minutes 13.30 seconds (8353.30 seconds total)