Starting phenix.real_space_refine on Thu Jan 16 10:21:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p5e_17449/01_2025/8p5e_17449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p5e_17449/01_2025/8p5e_17449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p5e_17449/01_2025/8p5e_17449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p5e_17449/01_2025/8p5e_17449.map" model { file = "/net/cci-nas-00/data/ceres_data/8p5e_17449/01_2025/8p5e_17449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p5e_17449/01_2025/8p5e_17449.cif" } resolution = 3.9 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= 0.001 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 42 5.49 5 Mg 3 5.21 5 S 239 5.16 5 C 33766 2.51 5 N 9210 2.21 5 O 10147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 53414 Number of models: 1 Model: "" Number of chains: 22 Chain: "2" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5235 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 636} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "3" Number of atoms: 5067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5067 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "4" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4702 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 568} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "5" Number of atoms: 5461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5461 Classifications: {'peptide': 695} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 668} Chain breaks: 5 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "6" Number of atoms: 5032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5032 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 21, 'TRANS': 614} Chain breaks: 3 Chain: "7" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5223 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 30, 'TRANS': 632} Chain breaks: 2 Chain: "A" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain breaks: 2 Chain: "D" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2014 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 229} Chain: "E" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4282 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 14, 'TRANS': 534} Chain breaks: 4 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 116 Chain: "F" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4381 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 30, 'TRANS': 517} Chain breaks: 3 Chain: "G" Number of atoms: 6628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 6628 Classifications: {'peptide': 825} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 32, 'TRANS': 792} Chain breaks: 8 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "H" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1663 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1591 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain breaks: 1 Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" 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 1330 SG CYS 2 344 25.447 63.046 154.888 1.00224.22 S ATOM 1509 SG CYS 2 367 27.197 66.155 157.479 1.00257.24 S ATOM 11543 SG CYS 4 349 41.407 80.085 190.685 1.00157.78 S ATOM 11564 SG CYS 4 352 39.868 81.672 192.204 1.00158.79 S ATOM 11711 SG CYS 4 371 40.900 77.380 191.816 1.00183.57 S ATOM 11753 SG CYS 4 376 38.166 79.008 192.819 1.00191.52 S ATOM 16196 SG CYS 5 186 47.077 39.852 151.274 1.00158.37 S ATOM 16384 SG CYS 5 211 45.108 41.371 151.412 1.00178.35 S ATOM 21739 SG CYS 6 311 31.954 78.144 171.205 1.00155.95 S ATOM 21952 SG CYS 6 338 28.943 76.098 172.080 1.00156.02 S ATOM 27105 SG CYS 7 262 62.111 58.351 193.822 1.00196.25 S ATOM 27128 SG CYS 7 265 61.883 56.821 196.992 1.00193.60 S ATOM 49065 SG CYS G2108 90.196 126.429 48.302 1.00145.03 S ATOM 49241 SG CYS G2130 88.102 128.273 51.110 1.00142.38 S ATOM 49265 SG CYS G2133 88.779 129.752 47.939 1.00132.20 S ATOM 49528 SG CYS G2164 92.044 94.975 86.175 1.00 87.86 S ATOM 49551 SG CYS G2167 94.390 96.632 88.818 1.00 93.20 S ATOM 49652 SG CYS G2179 95.261 93.284 87.299 1.00100.50 S Time building chain proxies: 21.79, per 1000 atoms: 0.41 Number of scatterers: 53414 At special positions: 0 Unit cell: (147.96, 170.64, 231.12, 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 239 16.00 P 42 15.00 Mg 3 11.99 O 10147 8.00 N 9210 7.00 C 33766 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: 9.77 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 902 " pdb="ZN ZN 2 902 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 2 902 " - pdb=" SG CYS 2 344 " pdb=" ZN 41002 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 349 " pdb=" ZN 5 802 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 211 " pdb=" ZN 61102 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 311 " pdb=" ZN 7 903 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 262 " pdb=" ZN G3001 " pdb="ZN ZN G3001 " - pdb=" SG CYS G2108 " pdb="ZN ZN G3001 " - pdb=" SG CYS G2133 " pdb="ZN ZN G3001 " - pdb=" SG CYS G2130 " pdb=" ZN G3002 " pdb="ZN ZN G3002 " - pdb=" SG CYS G2167 " pdb="ZN ZN G3002 " - pdb=" SG CYS G2164 " pdb="ZN ZN G3002 " - pdb=" SG CYS G2179 " Number of angles added : 6 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12626 Finding SS restraints... Secondary structure from input PDB file: 255 helices and 58 sheets defined 46.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain '2' and resid 182 through 187 Processing helix chain '2' and resid 193 through 199 removed outlier: 3.744A pdb=" N THR 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 200 through 218 removed outlier: 3.687A pdb=" N ARG 2 205 " --> pdb=" O PRO 2 201 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU 2 217 " --> pdb=" O SER 2 213 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 238 removed outlier: 3.683A pdb=" N ALA 2 229 " --> pdb=" O SER 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 252 removed outlier: 3.507A pdb=" N SER 2 252 " --> pdb=" O HIS 2 248 " (cutoff:3.500A) Processing helix chain '2' and resid 253 through 263 removed outlier: 3.562A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 3.601A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 289 removed outlier: 3.566A pdb=" N ARG 2 288 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 364 through 368 removed outlier: 3.957A pdb=" N CYS 2 367 " --> pdb=" O CYS 2 364 " (cutoff:3.500A) Processing helix chain '2' and resid 436 through 443 Processing helix chain '2' and resid 477 through 488 Processing helix chain '2' and resid 492 through 500 Processing helix chain '2' and resid 508 through 521 removed outlier: 3.940A pdb=" N ALA 2 516 " --> pdb=" O LYS 2 512 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 560 Processing helix chain '2' and resid 569 through 571 No H-bonds generated for 'chain '2' and resid 569 through 571' Processing helix chain '2' and resid 572 through 577 Processing helix chain '2' and resid 594 through 599 removed outlier: 3.717A pdb=" N LEU 2 598 " --> pdb=" O GLY 2 594 " (cutoff:3.500A) Processing helix chain '2' and resid 613 through 619 removed outlier: 4.181A pdb=" N THR 2 618 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER 2 619 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) Processing helix chain '2' and resid 620 through 625 Processing helix chain '2' and resid 652 through 656 removed outlier: 3.944A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 666 Processing helix chain '2' and resid 670 through 676 removed outlier: 4.030A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 689 through 706 Processing helix chain '2' and resid 739 through 754 removed outlier: 3.965A pdb=" N GLU 2 754 " --> pdb=" O LYS 2 750 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 773 Processing helix chain '2' and resid 782 through 795 Processing helix chain '2' and resid 796 through 800 Processing helix chain '2' and resid 807 through 824 removed outlier: 3.506A pdb=" N GLU 2 811 " --> pdb=" O VAL 2 807 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 Processing helix chain '2' and resid 853 through 861 Processing helix chain '3' and resid 19 through 35 removed outlier: 3.533A pdb=" N PHE 3 35 " --> pdb=" O PHE 3 31 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 52 Processing helix chain '3' and resid 100 through 107 Processing helix chain '3' and resid 107 through 117 removed outlier: 3.576A pdb=" N TRP 3 111 " --> pdb=" O ASP 3 107 " (cutoff:3.500A) 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 137 Processing helix chain '3' and resid 172 through 176 Processing helix chain '3' and resid 343 through 355 Processing helix chain '3' and resid 358 through 366 removed outlier: 3.810A pdb=" N ILE 3 362 " --> pdb=" O ASP 3 358 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 386 removed outlier: 3.788A pdb=" N MET 3 386 " --> pdb=" O LEU 3 382 " (cutoff:3.500A) Processing helix chain '3' and resid 415 through 426 Processing helix chain '3' and resid 439 through 443 removed outlier: 3.757A pdb=" N THR 3 443 " --> pdb=" O GLY 3 439 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 439 through 443' Processing helix chain '3' and resid 460 through 465 removed outlier: 3.675A pdb=" N ALA 3 465 " --> pdb=" O ALA 3 461 " (cutoff:3.500A) Processing helix chain '3' and resid 474 through 478 Processing helix chain '3' and resid 479 through 492 removed outlier: 3.555A pdb=" N ARG 3 483 " --> pdb=" O THR 3 479 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL 3 484 " --> pdb=" O ASP 3 480 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 541 Processing helix chain '3' and resid 554 through 570 removed outlier: 3.595A pdb=" N ARG 3 570 " --> pdb=" O LEU 3 566 " (cutoff:3.500A) Processing helix chain '3' and resid 652 through 667 removed outlier: 3.674A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL 3 667 " --> pdb=" O ALA 3 663 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 688 Processing helix chain '3' and resid 699 through 716 removed outlier: 4.093A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 3.649A pdb=" N ALA 3 726 " --> pdb=" O ASN 3 722 " (cutoff:3.500A) Processing helix chain '4' and resid 188 through 201 removed outlier: 4.064A pdb=" N THR 4 192 " --> pdb=" O GLN 4 188 " (cutoff:3.500A) Processing helix chain '4' and resid 203 through 211 Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 253 through 264 removed outlier: 4.046A pdb=" N LEU 4 257 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 removed outlier: 4.118A pdb=" N VAL 4 281 " --> pdb=" O LYS 4 277 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 299 removed outlier: 3.756A pdb=" N GLU 4 297 " --> pdb=" O LEU 4 293 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR 4 298 " --> pdb=" O ASP 4 294 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS 4 299 " --> pdb=" O GLU 4 295 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 293 through 299' Processing helix chain '4' and resid 318 through 322 removed outlier: 3.516A pdb=" N ILE 4 322 " --> pdb=" O PRO 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 386 through 389 removed outlier: 3.878A pdb=" N CYS 4 389 " --> pdb=" O HIS 4 386 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 386 through 389' Processing helix chain '4' and resid 403 through 406 Processing helix chain '4' and resid 422 through 424 No H-bonds generated for 'chain '4' and resid 422 through 424' Processing helix chain '4' and resid 505 through 514 Processing helix chain '4' and resid 517 through 525 Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 removed outlier: 3.871A pdb=" N ILE 4 577 " --> pdb=" O SER 4 573 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS 4 583 " --> pdb=" O GLN 4 579 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 639 through 652 removed outlier: 3.858A pdb=" N SER 4 643 " --> pdb=" O ASP 4 639 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU 4 650 " --> pdb=" O HIS 4 646 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN 4 651 " --> pdb=" O GLU 4 647 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 removed outlier: 4.208A pdb=" N ASN 4 691 " --> pdb=" O PRO 4 687 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 701 Processing helix chain '4' and resid 713 through 729 Processing helix chain '4' and resid 745 through 758 Processing helix chain '4' and resid 763 through 781 removed outlier: 3.731A pdb=" N LYS 4 767 " --> pdb=" O THR 4 763 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 811 removed outlier: 3.555A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) 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 835 removed outlier: 3.626A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP 4 835 " --> pdb=" O SER 4 831 " (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: 4.060A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 103 Proline residue: 5 88 - end of helix removed outlier: 4.004A pdb=" N THR 5 95 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 Processing helix chain '5' and resid 152 through 156 removed outlier: 3.622A pdb=" N VAL 5 156 " --> pdb=" O SER 5 153 " (cutoff:3.500A) Processing helix chain '5' and resid 261 through 265 Processing helix chain '5' and resid 281 through 283 No H-bonds generated for 'chain '5' and resid 281 through 283' Processing helix chain '5' and resid 350 through 362 Processing helix chain '5' and resid 365 through 374 Processing helix chain '5' and resid 382 through 394 Processing helix chain '5' and resid 422 through 433 removed outlier: 3.685A pdb=" N PHE 5 428 " --> pdb=" O GLN 5 424 " (cutoff:3.500A) Processing helix chain '5' and resid 487 through 491 removed outlier: 3.850A pdb=" N VAL 5 491 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) Processing helix chain '5' and resid 492 through 499 removed outlier: 4.237A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 550 removed outlier: 3.581A pdb=" N LEU 5 547 " --> pdb=" O GLN 5 543 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 579 through 588 removed outlier: 3.535A pdb=" N MET 5 583 " --> pdb=" O ASN 5 579 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 5 588 " --> pdb=" O GLN 5 584 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 641 removed outlier: 3.568A pdb=" N GLU 5 639 " --> pdb=" O ILE 5 635 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 667 removed outlier: 3.645A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 690 removed outlier: 3.664A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) Processing helix chain '5' and resid 708 through 722 Processing helix chain '5' and resid 730 through 740 Processing helix chain '5' and resid 742 through 758 removed outlier: 4.031A pdb=" N LEU 5 746 " --> pdb=" O ARG 5 742 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP 5 749 " --> pdb=" O GLN 5 745 " (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 160 removed outlier: 3.748A pdb=" N MET 6 160 " --> pdb=" O GLN 6 156 " (cutoff:3.500A) Processing helix chain '6' and resid 162 through 165 Processing helix chain '6' and resid 166 through 173 removed outlier: 3.614A pdb=" N GLN 6 173 " --> pdb=" O ALA 6 169 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 198 Processing helix chain '6' and resid 275 through 279 Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 382 through 386 removed outlier: 3.937A pdb=" N SER 6 385 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL 6 386 " --> pdb=" O GLY 6 383 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 382 through 386' Processing helix chain '6' and resid 501 through 507 removed outlier: 3.690A pdb=" N SER 6 507 " --> pdb=" O VAL 6 503 " (cutoff:3.500A) Processing helix chain '6' and resid 509 through 522 removed outlier: 3.909A pdb=" N LEU 6 516 " --> pdb=" O GLU 6 512 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 532 removed outlier: 4.234A pdb=" N ARG 6 531 " --> pdb=" O ASP 6 527 " (cutoff:3.500A) Processing helix chain '6' and resid 540 through 553 removed outlier: 3.681A pdb=" N LYS 6 544 " --> pdb=" O HIS 6 540 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS 6 545 " --> pdb=" O GLU 6 541 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 592 removed outlier: 3.696A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 621 removed outlier: 4.236A pdb=" N TYR 6 621 " --> pdb=" O GLY 6 618 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 618 through 621' Processing helix chain '6' and resid 626 through 632 Processing helix chain '6' and resid 645 through 659 removed outlier: 3.894A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU 6 657 " --> pdb=" O HIS 6 653 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 709 removed outlier: 3.675A pdb=" N MET 6 706 " --> pdb=" O THR 6 702 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER 6 707 " --> pdb=" O ALA 6 703 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 736 removed outlier: 3.512A pdb=" N ASP 6 724 " --> pdb=" O ASN 6 720 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR 6 725 " --> pdb=" O GLU 6 721 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU 6 726 " --> pdb=" O LYS 6 722 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU 6 734 " --> pdb=" O HIS 6 730 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS 6 735 " --> pdb=" O ILE 6 731 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 759 Processing helix chain '6' and resid 766 through 786 Processing helix chain '6' and resid 796 through 814 removed outlier: 3.766A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 840 removed outlier: 3.689A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL 6 838 " --> pdb=" O SER 6 834 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP 6 839 " --> pdb=" O ILE 6 835 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 28 removed outlier: 3.882A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 3.659A pdb=" N LYS 7 69 " --> pdb=" O ALA 7 65 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 93 Processing helix chain '7' and resid 102 through 109 Processing helix chain '7' and resid 110 through 124 Processing helix chain '7' and resid 133 through 136 Processing helix chain '7' and resid 137 through 151 Processing helix chain '7' and resid 152 through 154 No H-bonds generated for 'chain '7' and resid 152 through 154' Processing helix chain '7' and resid 193 through 197 Processing helix chain '7' and resid 208 through 215 removed outlier: 3.825A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 286 through 291 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 359 through 363 removed outlier: 4.213A pdb=" N GLY 7 362 " --> pdb=" O PRO 7 359 " (cutoff:3.500A) Processing helix chain '7' and resid 388 through 392 removed outlier: 3.946A pdb=" N PHE 7 391 " --> pdb=" O PHE 7 388 " (cutoff:3.500A) Processing helix chain '7' and resid 394 through 407 Processing helix chain '7' and resid 410 through 417 Processing helix chain '7' and resid 425 through 438 removed outlier: 3.594A pdb=" N LYS 7 429 " --> pdb=" O ASN 7 425 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY 7 438 " --> pdb=" O LEU 7 434 " (cutoff:3.500A) Processing helix chain '7' and resid 444 through 448 removed outlier: 3.668A pdb=" N MET 7 448 " --> pdb=" O GLY 7 445 " (cutoff:3.500A) Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 530 through 540 Processing helix chain '7' and resid 541 through 544 Processing helix chain '7' and resid 578 through 583 Processing helix chain '7' and resid 587 through 594 removed outlier: 3.530A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 3.650A pdb=" N ASP 7 609 " --> pdb=" O SER 7 605 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 649 removed outlier: 3.701A pdb=" N ALA 7 643 " --> pdb=" O ARG 7 639 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG 7 649 " --> pdb=" O ALA 7 645 " (cutoff:3.500A) Processing helix chain '7' and resid 655 through 672 removed outlier: 4.573A pdb=" N TYR 7 659 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) Processing helix chain '7' and resid 673 through 677 removed outlier: 3.590A pdb=" N SER 7 677 " --> pdb=" O GLU 7 674 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 703 removed outlier: 3.938A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 726 removed outlier: 3.517A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.750A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 removed outlier: 3.581A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.928A pdb=" N ILE C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 101' Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'C' and resid 117 through 141 removed outlier: 3.757A pdb=" N ALA C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 167 removed outlier: 4.363A pdb=" N SER C 163 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 192 removed outlier: 3.521A pdb=" N LYS C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.596A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 112 removed outlier: 3.810A pdb=" N MET D 84 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 154 removed outlier: 3.993A pdb=" N LEU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 170 through 175 removed outlier: 3.944A pdb=" N LEU D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 198 Processing helix chain 'D' and resid 199 through 202 Processing helix chain 'D' and resid 282 through 288 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 19 removed outlier: 3.575A pdb=" N ALA E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 52 removed outlier: 3.589A pdb=" N LEU E 39 " --> pdb=" O ASN E 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.112A pdb=" N ALA E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 159 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.669A pdb=" N ILE E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.511A pdb=" N GLN E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 284 through 302 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 333 through 341 Processing helix chain 'E' and resid 341 through 349 Processing helix chain 'E' and resid 352 through 367 removed outlier: 3.753A pdb=" N LYS E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 396 removed outlier: 5.113A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 421 through 434 Processing helix chain 'E' and resid 463 through 483 removed outlier: 3.573A pdb=" N VAL E 474 " --> pdb=" O ARG E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 517 removed outlier: 3.785A pdb=" N ARG E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 512 " --> pdb=" O ASN E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 540 removed outlier: 3.646A pdb=" N ARG E 540 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 558 Processing helix chain 'E' and resid 604 through 616 Processing helix chain 'E' and resid 636 through 647 Processing helix chain 'F' and resid 13 through 27 removed outlier: 3.631A pdb=" N LEU F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.626A pdb=" N VAL F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 47 Processing helix chain 'F' and resid 56 through 71 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 195 through 200 removed outlier: 3.619A pdb=" N ASN F 199 " --> pdb=" O ASN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 231 removed outlier: 4.015A pdb=" N VAL F 215 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE F 218 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 removed outlier: 3.824A pdb=" N LEU F 275 " --> pdb=" O LYS F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 358 removed outlier: 3.535A pdb=" N THR F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR F 358 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 392 removed outlier: 4.404A pdb=" N LYS F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE F 385 " --> pdb=" O LYS F 381 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 392 " --> pdb=" O HIS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 425 Processing helix chain 'F' and resid 453 through 470 removed outlier: 3.684A pdb=" N PHE F 462 " --> pdb=" O PHE F 458 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU F 465 " --> pdb=" O ASN F 461 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER F 470 " --> pdb=" O ALA F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 489 through 497 removed outlier: 4.042A pdb=" N VAL F 495 " --> pdb=" O TRP F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 513 Processing helix chain 'F' and resid 515 through 520 Processing helix chain 'F' and resid 546 through 553 Processing helix chain 'F' and resid 595 through 610 removed outlier: 3.871A pdb=" N THR F 599 " --> pdb=" O LYS F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 631 removed outlier: 3.992A pdb=" N HIS F 628 " --> pdb=" O ASP F 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 1403 through 1411 Processing helix chain 'G' and resid 1432 through 1441 Processing helix chain 'G' and resid 1455 through 1461 removed outlier: 3.726A pdb=" N GLN G1461 " --> pdb=" O LYS G1457 " (cutoff:3.500A) Processing helix chain 'G' and resid 1524 through 1539 Processing helix chain 'G' and resid 1539 through 1547 Processing helix chain 'G' and resid 1571 through 1584 removed outlier: 3.752A pdb=" N GLN G1575 " --> pdb=" O ARG G1571 " (cutoff:3.500A) Processing helix chain 'G' and resid 1596 through 1604 Processing helix chain 'G' and resid 1605 through 1610 removed outlier: 3.585A pdb=" N ASN G1608 " --> pdb=" O ARG G1605 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET G1610 " --> pdb=" O LEU G1607 " (cutoff:3.500A) Processing helix chain 'G' and resid 1626 through 1657 removed outlier: 4.182A pdb=" N THR G1630 " --> pdb=" O ASN G1626 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY G1643 " --> pdb=" O VAL G1639 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER G1644 " --> pdb=" O LEU G1640 " (cutoff:3.500A) Processing helix chain 'G' and resid 1667 through 1682 removed outlier: 3.758A pdb=" N ILE G1671 " --> pdb=" O SER G1667 " (cutoff:3.500A) Processing helix chain 'G' and resid 1700 through 1704 Processing helix chain 'G' and resid 1706 through 1715 Processing helix chain 'G' and resid 1738 through 1747 removed outlier: 3.595A pdb=" N SER G1747 " --> pdb=" O THR G1743 " (cutoff:3.500A) Processing helix chain 'G' and resid 1784 through 1804 Processing helix chain 'G' and resid 1806 through 1822 removed outlier: 4.569A pdb=" N ALA G1817 " --> pdb=" O VAL G1813 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER G1818 " --> pdb=" O ASN G1814 " (cutoff:3.500A) Processing helix chain 'G' and resid 1829 through 1854 removed outlier: 4.079A pdb=" N LEU G1854 " --> pdb=" O GLU G1850 " (cutoff:3.500A) Processing helix chain 'G' and resid 1874 through 1877 Processing helix chain 'G' and resid 1878 through 1892 Processing helix chain 'G' and resid 1893 through 1896 removed outlier: 3.523A pdb=" N SER G1896 " --> pdb=" O PRO G1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1893 through 1896' Processing helix chain 'G' and resid 1941 through 1945 Processing helix chain 'G' and resid 1949 through 1975 Processing helix chain 'G' and resid 2002 through 2006 removed outlier: 3.711A pdb=" N HIS G2005 " --> pdb=" O GLY G2002 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G2006 " --> pdb=" O PHE G2003 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2002 through 2006' Processing helix chain 'G' and resid 2007 through 2026 Processing helix chain 'G' and resid 2049 through 2064 removed outlier: 3.749A pdb=" N GLU G2053 " --> pdb=" O ASN G2049 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET G2062 " --> pdb=" O LEU G2058 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU G2064 " --> pdb=" O HIS G2060 " (cutoff:3.500A) Processing helix chain 'G' and resid 2068 through 2083 removed outlier: 3.671A pdb=" N ILE G2082 " --> pdb=" O GLU G2078 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE G2083 " --> pdb=" O LEU G2079 " (cutoff:3.500A) Processing helix chain 'G' and resid 2089 through 2093 Processing helix chain 'G' and resid 2138 through 2159 removed outlier: 3.589A pdb=" N LEU G2142 " --> pdb=" O ASN G2138 " (cutoff:3.500A) Processing helix chain 'G' and resid 2190 through 2208 removed outlier: 3.888A pdb=" N ILE G2194 " --> pdb=" O PRO G2190 " (cutoff:3.500A) Processing helix chain 'G' and resid 2210 through 2219 Processing helix chain 'H' and resid 3 through 24 removed outlier: 3.882A pdb=" N ASN H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 61 Processing helix chain 'H' and resid 64 through 104 removed outlier: 3.605A pdb=" N LEU H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN H 103 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN H 104 " --> pdb=" O MET H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 142 removed outlier: 3.871A pdb=" N LYS H 142 " --> pdb=" O ILE H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 203 removed outlier: 3.950A pdb=" N GLU H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU H 199 " --> pdb=" O ASP H 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 22 Processing helix chain 'I' and resid 56 through 62 removed outlier: 4.381A pdb=" N LEU I 60 " --> pdb=" O ASP I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 82 Processing helix chain 'I' and resid 94 through 108 removed outlier: 3.913A pdb=" N ARG I 100 " --> pdb=" O LYS I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 130 Processing helix chain 'I' and resid 137 through 160 removed outlier: 3.649A pdb=" N LEU I 141 " --> pdb=" O PRO I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 200 removed outlier: 3.541A pdb=" N LEU I 181 " --> pdb=" O GLU I 177 " (cutoff:3.500A) Proline residue: I 183 - end of helix removed outlier: 3.512A pdb=" N LEU I 200 " --> pdb=" O HIS I 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 243 through 244 Processing sheet with id=AA2, first strand: chain '2' and resid 331 through 332 removed outlier: 3.558A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA 2 453 " --> pdb=" O GLU 2 407 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE 2 409 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N SER 2 455 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG 2 458 " --> pdb=" O GLU 2 423 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLU 2 423 " --> pdb=" O ARG 2 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 346 through 347 Processing sheet with id=AA4, first strand: chain '2' and resid 525 through 527 Processing sheet with id=AA5, first strand: chain '2' and resid 563 through 567 removed outlier: 6.380A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA 2 566 " --> pdb=" O ASP 2 607 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU 2 542 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 579 through 582 Processing sheet with id=AA7, first strand: chain '2' and resid 628 through 633 removed outlier: 3.750A pdb=" N ILE 2 629 " --> pdb=" O LEU 2 640 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 96 through 99 Processing sheet with id=AA9, first strand: chain '3' and resid 165 through 166 removed outlier: 3.832A pdb=" N GLU 3 183 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS 3 178 " --> pdb=" O PHE 3 298 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE 3 298 " --> pdb=" O LYS 3 178 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ARG 3 291 " --> pdb=" O PRO 3 328 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN 3 293 " --> pdb=" O VAL 3 326 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL 3 326 " --> pdb=" O ASN 3 293 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL 3 295 " --> pdb=" O ASN 3 324 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU 3 301 " --> pdb=" O LYS 3 318 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS 3 318 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N THR 3 319 " --> pdb=" O SER 3 273 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP 3 275 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP 3 279 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR 3 325 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ARG 3 255 " --> pdb=" O THR 3 189 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR 3 189 " --> pdb=" O ARG 3 255 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR 3 257 " --> pdb=" O THR 3 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 195 through 196 Processing sheet with id=AB2, first strand: chain '3' and resid 242 through 243 removed outlier: 4.193A pdb=" N PHE 3 209 " --> pdb=" O ILE 7 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 391 through 393 removed outlier: 3.676A pdb=" N LYS 3 391 " --> pdb=" O LEU 3 399 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 429 through 433 removed outlier: 6.794A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 444 through 448 Processing sheet with id=AB6, first strand: chain '3' and resid 494 through 499 Processing sheet with id=AB7, first strand: chain '4' and resid 241 through 244 removed outlier: 7.010A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR 4 306 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU 4 243 " --> pdb=" O TYR 4 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '4' and resid 311 through 312 removed outlier: 4.843A pdb=" N LYS 4 329 " --> pdb=" O LYS 4 312 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 325 through 334 current: chain '4' and resid 354 through 359 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 354 through 359 current: chain '4' and resid 414 through 420 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 414 through 420 current: chain '4' and resid 457 through 468 Processing sheet with id=AB9, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AC1, first strand: chain '4' and resid 590 through 592 removed outlier: 3.538A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN 4 563 " --> pdb=" O LEU 4 704 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N TYR 4 706 " --> pdb=" O ASN 4 563 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 606 through 607 Processing sheet with id=AC3, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC4, first strand: chain '5' and resid 60 through 64 Processing sheet with id=AC5, first strand: chain '5' and resid 189 through 193 removed outlier: 8.093A pdb=" N SER 5 174 " --> pdb=" O PHE 5 250 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N PHE 5 250 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ALA 5 176 " --> pdb=" O SER 5 248 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N SER 5 248 " --> pdb=" O ALA 5 176 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N TYR 5 178 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLU 5 246 " --> pdb=" O TYR 5 178 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE 5 330 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ASP 5 279 " --> pdb=" O GLY 5 332 " (cutoff:3.500A) removed outlier: 13.029A pdb=" N GLN 5 334 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS 5 158 " --> pdb=" O TYR 5 298 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 398 through 399 removed outlier: 3.928A pdb=" N LYS 5 398 " --> pdb=" O LEU 5 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU 5 406 " --> pdb=" O LYS 5 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '5' and resid 436 through 440 removed outlier: 6.526A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 451 through 455 Processing sheet with id=AC9, first strand: chain '5' and resid 501 through 506 Processing sheet with id=AD1, first strand: chain '5' and resid 727 through 729 removed outlier: 3.604A pdb=" N THR 5 728 " --> pdb=" O ILE 5 770 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN 5 769 " --> pdb=" O ARG 5 764 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 150 through 154 Processing sheet with id=AD3, first strand: chain '6' and resid 287 through 296 removed outlier: 5.879A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG 6 296 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN 6 357 " --> pdb=" O LEU 6 381 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N THR 6 376 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N PHE 6 454 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP 6 378 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA 6 456 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE 6 380 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N HIS 6 458 " --> pdb=" O ILE 6 380 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER 6 453 " --> pdb=" O ILE 6 402 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER 6 461 " --> pdb=" O ARG 6 394 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ARG 6 394 " --> pdb=" O SER 6 461 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 303 through 310 removed outlier: 5.893A pdb=" N ALA 6 307 " --> pdb=" O ASN 6 320 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 557 through 558 removed outlier: 4.309A pdb=" N LYS 6 557 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '6' and resid 679 through 682 removed outlier: 6.483A pdb=" N ILE 6 571 " --> pdb=" O ALA 6 680 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA 6 682 " --> pdb=" O ILE 6 571 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL 6 573 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 596 through 599 removed outlier: 5.670A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER 6 677 " --> pdb=" O GLY 6 634 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '6' and resid 610 through 612 Processing sheet with id=AD9, first strand: chain '6' and resid 660 through 661 removed outlier: 3.575A pdb=" N ILE 6 661 " --> pdb=" O LEU 6 672 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AE2, first strand: chain '7' and resid 270 through 272 removed outlier: 8.063A pdb=" N PHE 7 307 " --> pdb=" O PRO 7 253 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N VAL 7 255 " --> pdb=" O SER 7 305 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N SER 7 305 " --> pdb=" O VAL 7 255 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N VAL 7 257 " --> pdb=" O ARG 7 303 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ARG 7 303 " --> pdb=" O VAL 7 257 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N THR 7 374 " --> pdb=" O SER 7 330 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN 7 332 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ASN 7 336 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N PHE 7 380 " --> pdb=" O ASN 7 336 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR 7 352 " --> pdb=" O GLN 7 379 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL 7 381 " --> pdb=" O ASP 7 350 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP 7 350 " --> pdb=" O VAL 7 381 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP 7 347 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY 7 243 " --> pdb=" O VAL 7 349 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR 7 246 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL 7 248 " --> pdb=" O GLU 7 312 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLU 7 312 " --> pdb=" O VAL 7 248 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '7' and resid 480 through 483 removed outlier: 6.062A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA 7 565 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 7 460 " --> pdb=" O ALA 7 567 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 43 through 47 Processing sheet with id=AE5, first strand: chain 'D' and resid 274 through 278 removed outlier: 3.507A pdb=" N TYR D 275 " --> pdb=" O ILE D 230 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 247 through 249 removed outlier: 3.812A pdb=" N ASN D 249 " --> pdb=" O LYS D 253 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LYS D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.054A pdb=" N ILE E 120 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL E 28 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL E 84 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE E 30 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU E 27 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL E 59 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 56 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN H 188 " --> pdb=" O ILE E 58 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 316 through 324 Processing sheet with id=AE9, first strand: chain 'E' and resid 520 through 521 removed outlier: 3.501A pdb=" N ALA E 570 " --> pdb=" O CYS E 528 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 171 through 174 removed outlier: 6.341A pdb=" N GLU F 538 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL F 640 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL F 540 " --> pdb=" O VAL F 640 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N CYS F 642 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE F 542 " --> pdb=" O CYS F 642 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET F 639 " --> pdb=" O ILE F 659 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 180 through 184 removed outlier: 4.302A pdb=" N ARG F 180 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN F 189 " --> pdb=" O ASN F 184 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.957A pdb=" N ILE F 313 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU F 329 " --> pdb=" O THR F 342 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET F 344 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU F 327 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL F 326 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY F 286 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY F 330 " --> pdb=" O PHE F 282 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP F 296 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N PHE F 339 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU F 306 " --> pdb=" O PHE F 339 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL F 341 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP F 308 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER F 343 " --> pdb=" O ASP F 308 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 399 through 401 removed outlier: 6.719A pdb=" N MET F 481 " --> pdb=" O VAL F 524 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 523 through 525 current: chain 'F' and resid 669 through 676 Processing sheet with id=AF5, first strand: chain 'G' and resid 1444 through 1445 removed outlier: 6.312A pdb=" N VAL G1324 " --> pdb=" O THR G1341 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR G1341 " --> pdb=" O VAL G1324 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N PHE G1463 " --> pdb=" O ASN G1348 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR G1350 " --> pdb=" O PHE G1463 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 1355 through 1360 Processing sheet with id=AF7, first strand: chain 'G' and resid 1500 through 1503 removed outlier: 3.518A pdb=" N GLN G1593 " --> pdb=" O LEU G1487 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU G1590 " --> pdb=" O VAL G1613 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 1508 through 1511 Processing sheet with id=AF9, first strand: chain 'G' and resid 1725 through 1727 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1725 through 1727 current: chain 'G' and resid 1865 through 1869 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1865 through 1869 current: chain 'G' and resid 1916 through 1922 Processing sheet with id=AG1, first strand: chain 'G' and resid 2102 through 2107 removed outlier: 4.019A pdb=" N ASP G2105 " --> pdb=" O SER G2115 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER G2115 " --> pdb=" O ASP G2105 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 2162 through 2164 Processing sheet with id=AG3, first strand: chain 'H' and resid 173 through 176 Processing sheet with id=AG4, first strand: chain 'I' and resid 24 through 27 2277 hydrogen bonds defined for protein. 6534 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: 20.73 Time building geometry restraints manager: 11.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17452 1.34 - 1.46: 10284 1.46 - 1.58: 26223 1.58 - 1.70: 68 1.70 - 1.82: 385 Bond restraints: 54412 Sorted by residual: bond pdb=" CB PRO F 634 " pdb=" CG PRO F 634 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.23e+00 bond pdb=" CB PRO I 4 " pdb=" CG PRO I 4 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" C LEU I 3 " pdb=" N PRO I 4 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.16e+00 bond pdb=" N ASN 6 340 " pdb=" CA ASN 6 340 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.84e+00 bond pdb=" CB TYR E 2 " pdb=" CG TYR E 2 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.20e-02 2.07e+03 1.64e+00 ... (remaining 54407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 72853 2.07 - 4.15: 771 4.15 - 6.22: 104 6.22 - 8.29: 9 8.29 - 10.36: 2 Bond angle restraints: 73739 Sorted by residual: angle pdb=" C ALA G1393 " pdb=" CA ALA G1393 " pdb=" CB ALA G1393 " ideal model delta sigma weight residual 115.79 110.37 5.42 1.19e+00 7.06e-01 2.07e+01 angle pdb=" N VAL 5 738 " pdb=" CA VAL 5 738 " pdb=" C VAL 5 738 " ideal model delta sigma weight residual 112.35 107.56 4.79 1.41e+00 5.03e-01 1.15e+01 angle pdb=" N ARG E 127 " pdb=" CA ARG E 127 " pdb=" C ARG E 127 " ideal model delta sigma weight residual 109.81 117.01 -7.20 2.21e+00 2.05e-01 1.06e+01 angle pdb=" N GLU G1537 " pdb=" CA GLU G1537 " pdb=" CB GLU G1537 " ideal model delta sigma weight residual 110.28 115.12 -4.84 1.55e+00 4.16e-01 9.75e+00 angle pdb=" C GLU 6 339 " pdb=" N ASN 6 340 " pdb=" CA ASN 6 340 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.58e+00 ... (remaining 73734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.86: 32344 31.86 - 63.72: 885 63.72 - 95.58: 85 95.58 - 127.45: 0 127.45 - 159.31: 2 Dihedral angle restraints: 33316 sinusoidal: 13882 harmonic: 19434 Sorted by residual: dihedral pdb=" O2A ADP 61101 " pdb=" O3A ADP 61101 " pdb=" PA ADP 61101 " pdb=" PB ADP 61101 " ideal model delta sinusoidal sigma weight residual -60.00 99.31 -159.31 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" CA THR 5 641 " pdb=" C THR 5 641 " pdb=" N GLU 5 642 " pdb=" CA GLU 5 642 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA CYS F 633 " pdb=" C CYS F 633 " pdb=" N PRO F 634 " pdb=" CA PRO F 634 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 33313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 5938 0.038 - 0.075: 1769 0.075 - 0.113: 657 0.113 - 0.151: 91 0.151 - 0.188: 12 Chirality restraints: 8467 Sorted by residual: chirality pdb=" CA PRO I 4 " pdb=" N PRO I 4 " pdb=" C PRO I 4 " pdb=" CB PRO I 4 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CB ILE F 204 " pdb=" CA ILE F 204 " pdb=" CG1 ILE F 204 " pdb=" CG2 ILE F 204 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA ARG E 127 " pdb=" N ARG E 127 " pdb=" C ARG E 127 " pdb=" CB ARG E 127 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 8464 not shown) Planarity restraints: 9332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 633 " -0.082 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO F 634 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO F 634 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO F 634 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 3 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO I 4 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO I 4 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO I 4 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 120 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C LEU I 120 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU I 120 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL I 121 " -0.016 2.00e-02 2.50e+03 ... (remaining 9329 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 319 2.52 - 3.12: 40821 3.12 - 3.71: 81762 3.71 - 4.31: 106824 4.31 - 4.90: 179604 Nonbonded interactions: 409330 Sorted by model distance: nonbonded pdb="MG MG 31001 " pdb=" O3B ATP 31002 " model vdw 1.929 2.170 nonbonded pdb="MG MG 31001 " pdb=" O1A ATP 31002 " model vdw 1.945 2.170 nonbonded pdb=" O1B ATP 7 901 " pdb="MG MG 7 902 " model vdw 1.956 2.170 nonbonded pdb="MG MG 31001 " pdb=" O2G ATP 31002 " model vdw 1.994 2.170 nonbonded pdb="MG MG 5 801 " pdb=" O1G ATP 5 803 " model vdw 1.999 2.170 ... (remaining 409325 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.520 Check model and map are aligned: 0.320 Set scattering table: 0.380 Process input model: 97.780 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.180 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:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.003 0.090 54412 Z= 0.186 Angle : 0.549 10.365 73739 Z= 0.287 Chirality : 0.042 0.188 8467 Planarity : 0.004 0.124 9332 Dihedral : 14.564 159.307 20690 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 6531 helix: 1.08 (0.10), residues: 2651 sheet: -0.16 (0.16), residues: 1081 loop : -1.06 (0.12), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 491 HIS 0.011 0.001 HIS 6 653 PHE 0.037 0.001 PHE G2201 TYR 0.038 0.001 TYR E 2 ARG 0.004 0.000 ARG 5 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 183 LEU cc_start: 0.8308 (tp) cc_final: 0.8059 (pp) REVERT: 3 384 MET cc_start: 0.9050 (tmm) cc_final: 0.8609 (tmm) REVERT: 4 199 MET cc_start: 0.8366 (mpp) cc_final: 0.7990 (mpp) REVERT: 4 342 MET cc_start: 0.8149 (tpt) cc_final: 0.7413 (tpt) REVERT: 4 382 MET cc_start: 0.7451 (tpp) cc_final: 0.7174 (mmm) REVERT: 4 421 ASP cc_start: 0.8476 (m-30) cc_final: 0.8188 (t0) REVERT: 4 777 MET cc_start: 0.8385 (ptt) cc_final: 0.8162 (ptp) REVERT: 4 801 MET cc_start: 0.8452 (ptp) cc_final: 0.8148 (ptp) REVERT: 6 609 THR cc_start: 0.8712 (p) cc_final: 0.8451 (p) REVERT: 6 706 MET cc_start: 0.8809 (mtm) cc_final: 0.8557 (mtt) REVERT: 7 506 MET cc_start: 0.2267 (mmp) cc_final: 0.0322 (ptp) REVERT: 7 507 ILE cc_start: 0.3298 (mt) cc_final: 0.2982 (mt) REVERT: 7 529 MET cc_start: 0.5584 (pmm) cc_final: 0.5369 (pmm) REVERT: 7 541 MET cc_start: 0.8524 (ppp) cc_final: 0.8155 (ppp) REVERT: 7 638 MET cc_start: 0.8182 (mpp) cc_final: 0.7629 (mpp) REVERT: 7 707 MET cc_start: 0.7261 (mmp) cc_final: 0.6951 (mpp) REVERT: C 7 ASP cc_start: 0.8770 (m-30) cc_final: 0.8243 (t0) REVERT: D 107 ASP cc_start: 0.7335 (p0) cc_final: 0.7082 (p0) REVERT: D 108 MET cc_start: 0.5980 (ptt) cc_final: 0.5284 (tmm) REVERT: E 366 MET cc_start: 0.8067 (mtm) cc_final: 0.7812 (mtt) REVERT: F 91 MET cc_start: 0.1818 (tpt) cc_final: 0.1512 (tpt) REVERT: F 481 MET cc_start: 0.7003 (tpt) cc_final: 0.6546 (tpp) REVERT: G 1351 PHE cc_start: 0.7913 (m-80) cc_final: 0.7636 (m-80) REVERT: G 1501 LEU cc_start: 0.7316 (pt) cc_final: 0.7038 (tt) REVERT: G 1542 LYS cc_start: 0.6138 (mttt) cc_final: 0.5538 (ptmt) REVERT: G 1668 MET cc_start: 0.8918 (mpp) cc_final: 0.8634 (pmm) REVERT: H 110 MET cc_start: 0.6481 (ptp) cc_final: 0.6033 (mtt) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.5225 time to fit residues: 342.4360 Evaluate side-chains 252 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 4.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 555 optimal weight: 0.0670 chunk 498 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 336 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 515 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 313 optimal weight: 2.9990 chunk 383 optimal weight: 6.9990 chunk 597 optimal weight: 9.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 528 ASN 3 564 HIS 6 156 GLN 6 157 HIS ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 107 GLN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.068961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.054691 restraints weight = 270852.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056365 restraints weight = 158812.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057005 restraints weight = 100206.673| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 54412 Z= 0.190 Angle : 0.576 9.949 73739 Z= 0.301 Chirality : 0.042 0.208 8467 Planarity : 0.004 0.123 9332 Dihedral : 9.483 165.242 7675 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 0.60 % Allowed : 6.57 % Favored : 92.83 % 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 (0.11), residues: 6531 helix: 1.23 (0.10), residues: 2734 sheet: -0.10 (0.16), residues: 1041 loop : -1.07 (0.12), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G1688 HIS 0.012 0.001 HIS 6 653 PHE 0.023 0.001 PHE G2201 TYR 0.023 0.001 TYR H 53 ARG 0.014 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 4.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 199 MET cc_start: 0.8288 (mpp) cc_final: 0.7858 (mpp) REVERT: 4 342 MET cc_start: 0.8207 (tpt) cc_final: 0.7551 (tpt) REVERT: 4 421 ASP cc_start: 0.8562 (m-30) cc_final: 0.8209 (t0) REVERT: 4 801 MET cc_start: 0.8505 (ptp) cc_final: 0.8240 (ptp) REVERT: 6 143 MET cc_start: 0.8320 (mpp) cc_final: 0.8098 (mpp) REVERT: 6 313 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7257 (ppp) REVERT: 7 506 MET cc_start: 0.2174 (mmp) cc_final: 0.0204 (ptp) REVERT: 7 538 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8126 (t-90) REVERT: 7 541 MET cc_start: 0.8623 (ppp) cc_final: 0.8242 (ppp) REVERT: 7 652 MET cc_start: 0.6154 (tmm) cc_final: 0.5813 (tmm) REVERT: 7 707 MET cc_start: 0.7279 (mmp) cc_final: 0.7024 (mpp) REVERT: C 7 ASP cc_start: 0.8768 (m-30) cc_final: 0.8246 (t0) REVERT: D 107 ASP cc_start: 0.7324 (p0) cc_final: 0.7099 (p0) REVERT: D 108 MET cc_start: 0.6234 (ptt) cc_final: 0.5669 (tmm) REVERT: D 277 MET cc_start: 0.8237 (tpp) cc_final: 0.7873 (mmt) REVERT: E 366 MET cc_start: 0.8137 (mtm) cc_final: 0.7899 (mtt) REVERT: F 481 MET cc_start: 0.6972 (tpt) cc_final: 0.6571 (tpp) REVERT: F 494 MET cc_start: 0.8380 (tpp) cc_final: 0.8148 (tpp) REVERT: G 1351 PHE cc_start: 0.7849 (m-80) cc_final: 0.7540 (m-80) REVERT: G 1501 LEU cc_start: 0.7287 (pt) cc_final: 0.7023 (tt) REVERT: G 1542 LYS cc_start: 0.6101 (mttt) cc_final: 0.5515 (ptmt) REVERT: H 110 MET cc_start: 0.6469 (ptp) cc_final: 0.6190 (mtt) outliers start: 35 outliers final: 21 residues processed: 307 average time/residue: 0.4967 time to fit residues: 264.7281 Evaluate side-chains 270 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 668 SER Chi-restraints excluded: chain 2 residue 796 GLU Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 5 residue 348 MET Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 540 ILE Chi-restraints excluded: chain 6 residue 157 HIS Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 538 HIS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 451 optimal weight: 0.9980 chunk 295 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 139 optimal weight: 0.0470 chunk 588 optimal weight: 3.9990 chunk 305 optimal weight: 8.9990 chunk 499 optimal weight: 4.9990 chunk 545 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 418 optimal weight: 3.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 649 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 98 GLN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1369 GLN ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.068841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054415 restraints weight = 271823.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.055758 restraints weight = 155623.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056663 restraints weight = 106773.638| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 54412 Z= 0.188 Angle : 0.545 8.603 73739 Z= 0.284 Chirality : 0.042 0.195 8467 Planarity : 0.004 0.123 9332 Dihedral : 9.378 166.952 7675 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 0.80 % Allowed : 9.26 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6531 helix: 1.30 (0.10), residues: 2754 sheet: -0.03 (0.17), residues: 1004 loop : -1.10 (0.12), residues: 2773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G1688 HIS 0.011 0.001 HIS 6 653 PHE 0.038 0.001 PHE 6 122 TYR 0.035 0.001 TYR H 53 ARG 0.006 0.000 ARG H 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 4.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 278 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8115 (pp) REVERT: 4 199 MET cc_start: 0.8341 (mpp) cc_final: 0.7805 (mpp) REVERT: 4 365 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8708 (tp) REVERT: 4 421 ASP cc_start: 0.8617 (m-30) cc_final: 0.8250 (t0) REVERT: 4 749 MET cc_start: 0.8741 (ppp) cc_final: 0.8519 (ppp) REVERT: 4 777 MET cc_start: 0.8378 (ptt) cc_final: 0.8157 (ptt) REVERT: 4 780 MET cc_start: 0.8701 (mtt) cc_final: 0.8468 (mtm) REVERT: 4 801 MET cc_start: 0.8466 (ptp) cc_final: 0.8198 (ptp) REVERT: 6 143 MET cc_start: 0.8310 (mpp) cc_final: 0.7992 (mpp) REVERT: 6 313 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7268 (ppp) REVERT: 7 459 MET cc_start: 0.7491 (mmm) cc_final: 0.7039 (tpt) REVERT: 7 506 MET cc_start: 0.2339 (mmp) cc_final: 0.0338 (ptp) REVERT: 7 538 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.8160 (t-90) REVERT: 7 541 MET cc_start: 0.8492 (ppp) cc_final: 0.8151 (ppp) REVERT: C 7 ASP cc_start: 0.8822 (m-30) cc_final: 0.8318 (t0) REVERT: D 108 MET cc_start: 0.6230 (ptt) cc_final: 0.5647 (tmm) REVERT: E 366 MET cc_start: 0.8161 (mtm) cc_final: 0.7956 (mtt) REVERT: F 481 MET cc_start: 0.6930 (tpt) cc_final: 0.6558 (tpp) REVERT: F 494 MET cc_start: 0.8375 (tpp) cc_final: 0.8096 (tpp) REVERT: G 1351 PHE cc_start: 0.7857 (m-80) cc_final: 0.7573 (m-80) REVERT: G 1501 LEU cc_start: 0.7426 (pt) cc_final: 0.7131 (tt) REVERT: G 1535 MET cc_start: 0.6899 (ttt) cc_final: 0.5940 (tmm) REVERT: G 1542 LYS cc_start: 0.6073 (mttt) cc_final: 0.5483 (tttt) outliers start: 47 outliers final: 30 residues processed: 294 average time/residue: 0.4899 time to fit residues: 250.5814 Evaluate side-chains 272 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 4.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 355 SER Chi-restraints excluded: chain 2 residue 373 PHE Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 408 VAL Chi-restraints excluded: chain 2 residue 796 GLU Chi-restraints excluded: chain 3 residue 197 ILE Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 4 residue 365 ILE Chi-restraints excluded: chain 4 residue 719 GLU Chi-restraints excluded: chain 5 residue 348 MET Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 157 HIS Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 538 HIS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1879 TYR Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 92 TRP Chi-restraints excluded: chain I residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 613 optimal weight: 0.8980 chunk 643 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 631 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 410 optimal weight: 0.9990 chunk 583 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 703 HIS 6 340 ASN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.069065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054628 restraints weight = 269907.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.055973 restraints weight = 155464.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.056872 restraints weight = 106816.350| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 54412 Z= 0.157 Angle : 0.523 9.739 73739 Z= 0.271 Chirality : 0.041 0.196 8467 Planarity : 0.004 0.122 9332 Dihedral : 9.235 166.248 7675 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Rotamer: Outliers : 1.24 % Allowed : 10.39 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.11), residues: 6531 helix: 1.43 (0.10), residues: 2754 sheet: -0.04 (0.16), residues: 1010 loop : -1.03 (0.12), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G1688 HIS 0.011 0.001 HIS 6 653 PHE 0.019 0.001 PHE 7 391 TYR 0.014 0.001 TYR 7 63 ARG 0.004 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 264 time to evaluate : 4.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 342 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5701 (mt) REVERT: 3 278 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8044 (pp) REVERT: 3 360 PHE cc_start: 0.7784 (p90) cc_final: 0.7548 (p90) REVERT: 3 671 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8822 (pp) REVERT: 4 199 MET cc_start: 0.8349 (mpp) cc_final: 0.7739 (mpp) REVERT: 4 421 ASP cc_start: 0.8552 (m-30) cc_final: 0.8230 (t0) REVERT: 4 749 MET cc_start: 0.8751 (ppp) cc_final: 0.8513 (ppp) REVERT: 6 143 MET cc_start: 0.8325 (mpp) cc_final: 0.7975 (mpp) REVERT: 6 160 MET cc_start: 0.8349 (pmm) cc_final: 0.7883 (pmm) REVERT: 6 313 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7210 (ppp) REVERT: 6 706 MET cc_start: 0.8837 (mtm) cc_final: 0.8543 (mtm) REVERT: 7 541 MET cc_start: 0.8548 (ppp) cc_final: 0.8247 (ppp) REVERT: 7 652 MET cc_start: 0.6145 (tmm) cc_final: 0.5831 (tmm) REVERT: C 7 ASP cc_start: 0.8779 (m-30) cc_final: 0.8312 (t0) REVERT: D 108 MET cc_start: 0.6336 (ptt) cc_final: 0.5633 (tmm) REVERT: D 277 MET cc_start: 0.8243 (tpp) cc_final: 0.7924 (mmt) REVERT: D 289 ASP cc_start: 0.8297 (t0) cc_final: 0.8081 (t0) REVERT: G 1351 PHE cc_start: 0.7742 (m-80) cc_final: 0.7508 (m-80) REVERT: G 1501 LEU cc_start: 0.7290 (pt) cc_final: 0.7047 (tt) REVERT: G 1542 LYS cc_start: 0.6011 (mttt) cc_final: 0.5406 (tttt) outliers start: 73 outliers final: 35 residues processed: 318 average time/residue: 0.4836 time to fit residues: 268.7825 Evaluate side-chains 281 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 4.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 342 LEU Chi-restraints excluded: chain 2 residue 373 PHE Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 408 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 796 GLU Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 671 LEU Chi-restraints excluded: chain 4 residue 719 GLU Chi-restraints excluded: chain 5 residue 348 MET Chi-restraints excluded: chain 5 residue 360 LEU Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 540 ILE Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 579 THR Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1879 TYR Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 92 TRP Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 189 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 507 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 280 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 553 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 471 optimal weight: 1.9990 chunk 437 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 570 ASN 6 139 GLN 6 149 ASN ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 653 HIS 7 620 HIS ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 HIS ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 372 ASN G1461 GLN G1575 GLN ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN I 6 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.066621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052463 restraints weight = 276089.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054060 restraints weight = 168561.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.054587 restraints weight = 107567.107| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 54412 Z= 0.344 Angle : 0.656 11.100 73739 Z= 0.340 Chirality : 0.044 0.197 8467 Planarity : 0.005 0.123 9332 Dihedral : 9.562 172.894 7675 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 1.72 % Allowed : 12.07 % Favored : 86.21 % 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: -0.16 (0.10), residues: 6531 helix: 1.08 (0.10), residues: 2762 sheet: -0.29 (0.17), residues: 984 loop : -1.23 (0.11), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G1688 HIS 0.010 0.001 HIS 6 653 PHE 0.021 0.002 PHE 4 197 TYR 0.021 0.002 TYR 6 621 ARG 0.010 0.001 ARG F 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 244 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 501 MET cc_start: 0.7879 (mtm) cc_final: 0.7640 (ttm) REVERT: 2 764 MET cc_start: 0.8340 (mmt) cc_final: 0.8102 (mmt) REVERT: 2 783 MET cc_start: 0.7160 (tpp) cc_final: 0.6785 (tmm) REVERT: 3 174 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: 3 671 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8785 (pp) REVERT: 3 702 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6807 (tt) REVERT: 4 199 MET cc_start: 0.8427 (mpp) cc_final: 0.7848 (mpp) REVERT: 4 421 ASP cc_start: 0.8650 (m-30) cc_final: 0.8326 (t0) REVERT: 4 749 MET cc_start: 0.8866 (ppp) cc_final: 0.8627 (ppp) REVERT: 4 777 MET cc_start: 0.8509 (ptt) cc_final: 0.8287 (ptp) REVERT: 5 172 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7713 (mt) REVERT: 6 143 MET cc_start: 0.8314 (mpp) cc_final: 0.8057 (mpp) REVERT: 6 160 MET cc_start: 0.8449 (pmm) cc_final: 0.7924 (pmm) REVERT: 6 313 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7323 (ppp) REVERT: 7 541 MET cc_start: 0.8565 (ppp) cc_final: 0.8197 (ppp) REVERT: 7 652 MET cc_start: 0.6283 (tmm) cc_final: 0.5864 (tmm) REVERT: C 7 ASP cc_start: 0.8850 (m-30) cc_final: 0.8305 (t0) REVERT: D 108 MET cc_start: 0.6163 (ptt) cc_final: 0.5415 (tmm) REVERT: D 277 MET cc_start: 0.8291 (tpp) cc_final: 0.7640 (mmt) REVERT: F 72 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: F 414 MET cc_start: 0.8986 (mmt) cc_final: 0.8762 (mmt) REVERT: F 434 TRP cc_start: 0.7743 (m-10) cc_final: 0.7459 (m-10) REVERT: F 447 MET cc_start: 0.6347 (mmt) cc_final: 0.6043 (mmt) REVERT: I 52 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8864 (mt) outliers start: 101 outliers final: 64 residues processed: 323 average time/residue: 0.4808 time to fit residues: 272.2569 Evaluate side-chains 304 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 233 time to evaluate : 4.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 186 LEU Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 355 SER Chi-restraints excluded: chain 2 residue 373 PHE Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 408 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 668 SER Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 796 GLU Chi-restraints excluded: chain 3 residue 174 GLN Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 530 HIS Chi-restraints excluded: chain 3 residue 671 LEU Chi-restraints excluded: chain 3 residue 702 LEU Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 719 GLU Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 348 MET Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 526 ILE Chi-restraints excluded: chain 5 residue 540 ILE Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 157 HIS Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 579 THR Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 348 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 529 MET Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 372 ASN Chi-restraints excluded: chain G residue 1461 GLN Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1879 TYR Chi-restraints excluded: chain G residue 1885 MET Chi-restraints excluded: chain G residue 2039 VAL Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain G residue 2140 VAL Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 92 TRP Chi-restraints excluded: chain I residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 45 optimal weight: 1.9990 chunk 603 optimal weight: 0.9980 chunk 405 optimal weight: 0.0470 chunk 454 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 177 optimal weight: 0.0670 chunk 533 optimal weight: 10.0000 chunk 152 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 531 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 626 GLN ** 3 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 641 ASN 3 661 GLN ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 653 HIS ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.068774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054308 restraints weight = 269458.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.055634 restraints weight = 155628.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056541 restraints weight = 107245.325| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.002 0.090 54412 Z= 0.143 Angle : 0.551 12.141 73739 Z= 0.282 Chirality : 0.041 0.225 8467 Planarity : 0.004 0.121 9332 Dihedral : 9.247 173.818 7675 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 1.11 % Allowed : 13.69 % Favored : 85.20 % 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: 0.21 (0.11), residues: 6531 helix: 1.40 (0.10), residues: 2762 sheet: -0.11 (0.17), residues: 995 loop : -1.05 (0.12), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 129 HIS 0.009 0.001 HIS 6 653 PHE 0.020 0.001 PHE D 251 TYR 0.015 0.001 TYR 7 63 ARG 0.007 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 4.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 501 MET cc_start: 0.7973 (mtm) cc_final: 0.7512 (ttm) REVERT: 2 783 MET cc_start: 0.7287 (tpp) cc_final: 0.6983 (tmm) REVERT: 3 360 PHE cc_start: 0.7800 (p90) cc_final: 0.7554 (p90) REVERT: 3 671 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8686 (pp) REVERT: 4 199 MET cc_start: 0.8471 (mpp) cc_final: 0.7811 (mpp) REVERT: 4 421 ASP cc_start: 0.8664 (m-30) cc_final: 0.8254 (t0) REVERT: 4 749 MET cc_start: 0.8948 (ppp) cc_final: 0.8683 (ppp) REVERT: 4 811 MET cc_start: 0.8497 (ptt) cc_final: 0.8258 (ptm) REVERT: 5 172 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7759 (mt) REVERT: 6 143 MET cc_start: 0.8295 (mpp) cc_final: 0.8087 (mpp) REVERT: 6 160 MET cc_start: 0.8451 (pmm) cc_final: 0.7921 (pmm) REVERT: 6 313 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7066 (ppp) REVERT: 6 401 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: 6 644 MET cc_start: 0.7294 (ttm) cc_final: 0.7034 (ttm) REVERT: 7 459 MET cc_start: 0.7546 (mmm) cc_final: 0.7073 (tpt) REVERT: 7 541 MET cc_start: 0.8515 (ppp) cc_final: 0.8203 (ppp) REVERT: 7 652 MET cc_start: 0.5981 (tmm) cc_final: 0.5608 (tmm) REVERT: C 7 ASP cc_start: 0.8852 (m-30) cc_final: 0.8292 (t0) REVERT: D 108 MET cc_start: 0.6316 (ptt) cc_final: 0.5925 (tmm) REVERT: D 277 MET cc_start: 0.8210 (tpp) cc_final: 0.7610 (mmt) REVERT: D 289 ASP cc_start: 0.8212 (t0) cc_final: 0.8010 (t0) REVERT: F 72 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: F 414 MET cc_start: 0.9009 (mmt) cc_final: 0.8800 (mmt) REVERT: F 434 TRP cc_start: 0.7638 (m-10) cc_final: 0.7238 (m-10) REVERT: F 494 MET cc_start: 0.8294 (tpp) cc_final: 0.8048 (tpp) REVERT: I 14 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8365 (mm-30) REVERT: I 63 MET cc_start: 0.8051 (ptp) cc_final: 0.7571 (ptp) outliers start: 65 outliers final: 38 residues processed: 304 average time/residue: 0.4962 time to fit residues: 263.9813 Evaluate side-chains 283 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 4.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 373 PHE Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 796 GLU Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 671 LEU Chi-restraints excluded: chain 4 residue 280 MET Chi-restraints excluded: chain 4 residue 649 MET Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 348 MET Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 401 GLU Chi-restraints excluded: chain 6 residue 579 THR Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain G residue 1480 PHE Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 1620 VAL Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1879 TYR Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 92 TRP Chi-restraints excluded: chain I residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 520 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 657 optimal weight: 0.0060 chunk 422 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 524 optimal weight: 0.0980 chunk 39 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 576 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 540 optimal weight: 6.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 685 ASN 5 203 ASN ** 6 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 653 HIS 7 384 HIS ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.068489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054156 restraints weight = 270495.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055826 restraints weight = 160458.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056649 restraints weight = 98252.889| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 54412 Z= 0.163 Angle : 0.540 15.916 73739 Z= 0.277 Chirality : 0.041 0.201 8467 Planarity : 0.004 0.121 9332 Dihedral : 9.170 174.255 7675 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 1.14 % Allowed : 14.22 % Favored : 84.64 % 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: 0.26 (0.11), residues: 6531 helix: 1.45 (0.10), residues: 2764 sheet: -0.08 (0.17), residues: 1005 loop : -1.03 (0.12), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G1688 HIS 0.015 0.001 HIS 6 653 PHE 0.016 0.001 PHE D 251 TYR 0.014 0.001 TYR 7 63 ARG 0.006 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 4.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 501 MET cc_start: 0.7995 (mtm) cc_final: 0.7489 (ttm) REVERT: 2 783 MET cc_start: 0.7202 (tpp) cc_final: 0.6862 (tmm) REVERT: 3 360 PHE cc_start: 0.7910 (p90) cc_final: 0.7661 (p90) REVERT: 3 671 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8642 (pp) REVERT: 4 421 ASP cc_start: 0.8704 (m-30) cc_final: 0.8262 (t0) REVERT: 4 749 MET cc_start: 0.8984 (ppp) cc_final: 0.8718 (ppp) REVERT: 4 811 MET cc_start: 0.8568 (ptt) cc_final: 0.8350 (ptm) REVERT: 5 172 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7782 (mt) REVERT: 5 552 MET cc_start: 0.8587 (ttm) cc_final: 0.8165 (mtp) REVERT: 6 160 MET cc_start: 0.8450 (pmm) cc_final: 0.7955 (pmm) REVERT: 6 313 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7147 (ppp) REVERT: 6 401 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: 6 644 MET cc_start: 0.7279 (ttm) cc_final: 0.6980 (ttm) REVERT: 7 459 MET cc_start: 0.7516 (mmm) cc_final: 0.7061 (tpt) REVERT: 7 506 MET cc_start: 0.1953 (mmt) cc_final: -0.0327 (ptp) REVERT: 7 541 MET cc_start: 0.8527 (ppp) cc_final: 0.8211 (ppp) REVERT: 7 652 MET cc_start: 0.5897 (tmm) cc_final: 0.5690 (ppp) REVERT: C 7 ASP cc_start: 0.8872 (m-30) cc_final: 0.8317 (t0) REVERT: D 108 MET cc_start: 0.6554 (ptt) cc_final: 0.5982 (tmm) REVERT: D 129 MET cc_start: 0.8107 (mpp) cc_final: 0.7855 (mpp) REVERT: D 277 MET cc_start: 0.8351 (tpp) cc_final: 0.7560 (mmt) REVERT: D 289 ASP cc_start: 0.8320 (t0) cc_final: 0.8091 (t0) REVERT: F 72 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: F 434 TRP cc_start: 0.7732 (m-10) cc_final: 0.7311 (m-10) REVERT: F 494 MET cc_start: 0.8271 (tpp) cc_final: 0.8051 (tpp) REVERT: G 1535 MET cc_start: 0.6745 (ttt) cc_final: 0.5870 (tmm) REVERT: G 1732 LEU cc_start: 0.9037 (pt) cc_final: 0.8768 (pt) outliers start: 67 outliers final: 48 residues processed: 302 average time/residue: 0.5075 time to fit residues: 269.6375 Evaluate side-chains 295 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 4.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 342 LEU Chi-restraints excluded: chain 2 residue 373 PHE Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 668 SER Chi-restraints excluded: chain 2 residue 796 GLU Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 671 LEU Chi-restraints excluded: chain 4 residue 280 MET Chi-restraints excluded: chain 4 residue 649 MET Chi-restraints excluded: chain 4 residue 654 ILE Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 348 MET Chi-restraints excluded: chain 5 residue 360 LEU Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 540 ILE Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 157 HIS Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 401 GLU Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 579 THR Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain G residue 1480 PHE Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 1620 VAL Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1879 TYR Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 92 TRP Chi-restraints excluded: chain I residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 13 optimal weight: 7.9990 chunk 593 optimal weight: 0.0670 chunk 412 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 330 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 chunk 554 optimal weight: 20.0000 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 638 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** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.068064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053734 restraints weight = 272036.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055323 restraints weight = 161537.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056080 restraints weight = 101597.010| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 54412 Z= 0.197 Angle : 0.555 11.167 73739 Z= 0.285 Chirality : 0.041 0.200 8467 Planarity : 0.004 0.121 9332 Dihedral : 9.193 175.897 7675 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 1.33 % Allowed : 14.59 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.11), residues: 6531 helix: 1.46 (0.10), residues: 2752 sheet: -0.15 (0.16), residues: 1013 loop : -1.02 (0.12), residues: 2766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G1688 HIS 0.017 0.001 HIS 6 653 PHE 0.022 0.001 PHE G1351 TYR 0.016 0.001 TYR H 20 ARG 0.008 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13062 Ramachandran restraints generated. 6531 Oldfield, 0 Emsley, 6531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 245 time to evaluate : 4.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 501 MET cc_start: 0.8025 (mtm) cc_final: 0.7558 (ttm) REVERT: 2 783 MET cc_start: 0.7232 (tpp) cc_final: 0.6891 (tmm) REVERT: 3 360 PHE cc_start: 0.7940 (p90) cc_final: 0.7682 (p90) REVERT: 3 671 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8651 (pp) REVERT: 4 316 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6119 (mm-30) REVERT: 4 421 ASP cc_start: 0.8694 (m-30) cc_final: 0.8229 (t0) REVERT: 4 749 MET cc_start: 0.8995 (ppp) cc_final: 0.8720 (ppp) REVERT: 4 811 MET cc_start: 0.8581 (ptt) cc_final: 0.8372 (ptm) REVERT: 5 172 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7753 (mt) REVERT: 6 160 MET cc_start: 0.8451 (pmm) cc_final: 0.7924 (pmm) REVERT: 6 313 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7134 (ppp) REVERT: 6 401 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: 6 644 MET cc_start: 0.7495 (ttm) cc_final: 0.7173 (ttm) REVERT: 7 448 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6775 (mmt) REVERT: 7 506 MET cc_start: 0.1870 (mmt) cc_final: -0.0260 (ptp) REVERT: 7 541 MET cc_start: 0.8523 (ppp) cc_final: 0.8207 (ppp) REVERT: 7 652 MET cc_start: 0.5884 (tmm) cc_final: 0.5679 (ppp) REVERT: C 7 ASP cc_start: 0.8875 (m-30) cc_final: 0.8298 (t0) REVERT: D 108 MET cc_start: 0.6495 (ptt) cc_final: 0.5975 (tmm) REVERT: D 129 MET cc_start: 0.8160 (mpp) cc_final: 0.7915 (mpp) REVERT: D 277 MET cc_start: 0.8314 (tpp) cc_final: 0.7350 (mmt) REVERT: F 72 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: F 434 TRP cc_start: 0.7823 (m-10) cc_final: 0.7376 (m-10) REVERT: G 1535 MET cc_start: 0.6907 (ttt) cc_final: 0.5965 (tmm) REVERT: I 63 MET cc_start: 0.8241 (ptp) cc_final: 0.7820 (ptp) outliers start: 78 outliers final: 56 residues processed: 304 average time/residue: 0.4917 time to fit residues: 262.1863 Evaluate side-chains 305 residues out of total 5946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 215 LEU Chi-restraints excluded: chain 2 residue 342 LEU Chi-restraints excluded: chain 2 residue 373 PHE Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 408 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 668 SER Chi-restraints excluded: chain 2 residue 796 GLU Chi-restraints excluded: chain 3 residue 275 ASP Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 530 HIS Chi-restraints excluded: chain 3 residue 671 LEU Chi-restraints excluded: chain 4 residue 280 MET Chi-restraints excluded: chain 4 residue 316 GLU Chi-restraints excluded: chain 4 residue 649 MET Chi-restraints excluded: chain 4 residue 654 ILE Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 348 MET Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 157 HIS Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 401 GLU Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 579 THR Chi-restraints excluded: chain 6 residue 650 VAL Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 333 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 448 MET Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain G residue 1359 MET Chi-restraints excluded: chain G residue 1480 PHE Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 1615 LEU Chi-restraints excluded: chain G residue 1620 VAL Chi-restraints excluded: chain G residue 1707 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1879 TYR Chi-restraints excluded: chain G residue 2039 VAL Chi-restraints excluded: chain G residue 2098 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 92 TRP Chi-restraints excluded: chain I residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9859 > 50: distance: 57 - 62: 20.749 distance: 62 - 63: 23.586 distance: 63 - 64: 14.553 distance: 63 - 66: 18.406 distance: 64 - 65: 25.027 distance: 64 - 70: 21.141 distance: 66 - 67: 5.801 distance: 67 - 68: 34.923 distance: 67 - 69: 27.192 distance: 70 - 71: 44.510 distance: 71 - 72: 20.519 distance: 72 - 73: 25.967 distance: 72 - 74: 27.121 distance: 74 - 75: 20.526 distance: 75 - 76: 62.629 distance: 75 - 78: 44.232 distance: 76 - 83: 56.971 distance: 78 - 79: 10.114 distance: 79 - 80: 30.871 distance: 80 - 81: 38.091 distance: 80 - 82: 16.869 distance: 83 - 84: 33.501 distance: 84 - 85: 56.564 distance: 84 - 87: 45.142 distance: 85 - 86: 63.374 distance: 85 - 90: 34.674 distance: 87 - 88: 40.368 distance: 87 - 89: 4.108 distance: 90 - 91: 12.294 distance: 90 - 96: 32.287 distance: 91 - 92: 11.050 distance: 91 - 94: 32.713 distance: 92 - 93: 11.800 distance: 92 - 97: 6.339 distance: 94 - 95: 36.706 distance: 95 - 96: 27.942 distance: 97 - 98: 20.580 distance: 98 - 99: 12.034 distance: 98 - 101: 29.756 distance: 99 - 100: 18.480 distance: 99 - 107: 19.024 distance: 101 - 102: 36.029 distance: 102 - 103: 44.105 distance: 102 - 104: 43.117 distance: 103 - 105: 41.390 distance: 104 - 106: 53.785 distance: 105 - 106: 47.462 distance: 107 - 108: 11.883 distance: 108 - 109: 33.314 distance: 108 - 111: 25.650 distance: 109 - 110: 18.420 distance: 109 - 113: 12.554 distance: 111 - 112: 36.859 distance: 113 - 114: 24.482 distance: 114 - 115: 41.973 distance: 114 - 117: 11.654 distance: 115 - 116: 15.164 distance: 115 - 121: 33.693 distance: 117 - 118: 34.357 distance: 117 - 119: 19.349 distance: 118 - 120: 23.434 distance: 121 - 122: 8.926 distance: 122 - 123: 27.662 distance: 122 - 125: 26.978 distance: 123 - 124: 20.352 distance: 123 - 127: 29.157 distance: 125 - 126: 31.480 distance: 127 - 128: 40.186 distance: 128 - 129: 31.129 distance: 128 - 131: 31.109 distance: 129 - 130: 28.788 distance: 129 - 135: 22.994 distance: 131 - 132: 39.828 distance: 132 - 133: 7.255 distance: 132 - 134: 37.848