Starting phenix.real_space_refine on Tue Nov 19 18:15:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/11_2024/8p62_17458.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/11_2024/8p62_17458.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/11_2024/8p62_17458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/11_2024/8p62_17458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/11_2024/8p62_17458.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/11_2024/8p62_17458.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 25 5.49 5 Mg 3 5.21 5 S 239 5.16 5 C 33582 2.51 5 N 9141 2.21 5 O 10045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 53042 Number of models: 1 Model: "" Number of chains: 21 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: 5447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5447 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 666} 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: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} 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: 4276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4276 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 14, 'TRANS': 534} Chain breaks: 4 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 161 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': 10} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4379 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 30, 'TRANS': 517} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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 25.226 62.859 154.856 1.00270.01 S ATOM 1509 SG CYS 2 367 27.082 66.214 157.078 1.00297.77 S ATOM 11543 SG CYS 4 349 40.909 80.383 190.494 1.00152.25 S ATOM 11564 SG CYS 4 352 39.642 82.422 192.744 1.00157.34 S ATOM 11753 SG CYS 4 376 37.890 78.955 193.418 1.00175.35 S ATOM 16196 SG CYS 5 186 47.071 39.644 151.192 1.00144.24 S ATOM 16384 SG CYS 5 211 44.717 41.471 151.338 1.00171.28 S ATOM 21725 SG CYS 6 311 31.389 78.766 171.156 1.00140.48 S ATOM 21747 SG CYS 6 314 27.643 79.086 170.564 1.00139.86 S ATOM 21904 SG CYS 6 333 29.091 79.642 174.009 1.00132.00 S ATOM 21938 SG CYS 6 338 29.052 76.127 172.568 1.00147.67 S ATOM 27114 SG CYS 7 265 60.595 58.036 198.740 1.00183.21 S ATOM 27305 SG CYS 7 289 59.570 56.616 196.036 1.00214.17 S ATOM 48693 SG CYS G2108 90.210 126.679 48.483 1.00139.28 S ATOM 48720 SG CYS G2111 91.224 130.304 49.092 1.00141.35 S ATOM 48869 SG CYS G2130 88.195 128.588 51.063 1.00141.07 S ATOM 48893 SG CYS G2133 88.097 129.833 47.529 1.00138.32 S ATOM 49156 SG CYS G2164 92.103 94.940 86.221 1.00 99.89 S ATOM 49179 SG CYS G2167 94.682 96.785 88.092 1.00109.38 S ATOM 49280 SG CYS G2179 95.521 93.342 87.348 1.00104.99 S Time building chain proxies: 27.11, per 1000 atoms: 0.51 Number of scatterers: 53042 At special positions: 0 Unit cell: (149.04, 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 25 15.00 Mg 3 11.99 O 10045 8.00 N 9141 7.00 C 33582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.69 Conformation dependent library (CDL) restraints added in 6.6 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 4 349 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 352 " pdb=" ZN 51702 " pdb="ZN ZN 51702 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51702 " - pdb=" SG CYS 5 186 " pdb=" ZN 61102 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61102 " - pdb=" SG CYS 6 314 " pdb=" ZN 7 903 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 265 " pdb=" ZN G4001 " pdb="ZN ZN G4001 " - pdb=" SG CYS G2133 " pdb="ZN ZN G4001 " - pdb=" SG CYS G2111 " pdb="ZN ZN G4001 " - pdb=" SG CYS G2108 " pdb="ZN ZN G4001 " - pdb=" SG CYS G2130 " pdb=" ZN G4002 " pdb="ZN ZN G4002 " - pdb=" SG CYS G2167 " pdb="ZN ZN G4002 " - pdb=" SG CYS G2179 " pdb="ZN ZN G4002 " - pdb=" SG CYS G2164 " Number of angles added : 12 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12622 Finding SS restraints... Secondary structure from input PDB file: 256 helices and 58 sheets defined 46.2% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain '2' and resid 182 through 187 Processing helix chain '2' and resid 193 through 199 removed outlier: 3.857A pdb=" N THR 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 200 through 218 removed outlier: 3.608A pdb=" N ARG 2 205 " --> pdb=" O PRO 2 201 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 238 removed outlier: 3.578A pdb=" N ALA 2 229 " --> pdb=" O SER 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 252 Processing helix chain '2' and resid 253 through 263 removed outlier: 3.667A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 264 through 283 removed outlier: 3.885A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 289 removed outlier: 3.656A pdb=" N ARG 2 288 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 435 through 443 removed outlier: 3.863A pdb=" N ASN 2 439 " --> pdb=" O ASP 2 435 " (cutoff:3.500A) 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 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 removed outlier: 3.532A pdb=" N THR 2 577 " --> pdb=" O ALA 2 573 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 removed outlier: 3.591A pdb=" N LEU 2 598 " --> pdb=" O GLY 2 594 " (cutoff:3.500A) Processing helix chain '2' and resid 620 through 625 Processing helix chain '2' and resid 652 through 656 removed outlier: 3.981A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 666 Processing helix chain '2' and resid 670 through 675 Processing helix chain '2' and resid 688 through 706 removed outlier: 3.606A pdb=" N GLU 2 693 " --> pdb=" O GLU 2 689 " (cutoff:3.500A) Processing helix chain '2' and resid 739 through 754 removed outlier: 3.988A 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 806 through 824 removed outlier: 4.139A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 removed outlier: 3.714A pdb=" N LEU 2 834 " --> pdb=" O SER 2 830 " (cutoff:3.500A) Processing helix chain '2' and resid 853 through 861 Processing helix chain '2' and resid 862 through 864 No H-bonds generated for 'chain '2' and resid 862 through 864' Processing helix chain '3' and resid 19 through 35 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 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 145 through 149 removed outlier: 3.593A pdb=" N SER 3 148 " --> pdb=" O SER 3 145 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER 3 149 " --> pdb=" O ALA 3 146 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 145 through 149' Processing helix chain '3' and resid 161 through 163 No H-bonds generated for 'chain '3' and resid 161 through 163' Processing helix chain '3' and resid 172 through 176 Processing helix chain '3' and resid 343 through 355 Processing helix chain '3' and resid 358 through 367 removed outlier: 3.530A pdb=" N LEU 3 367 " --> pdb=" O LEU 3 363 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 386 removed outlier: 3.780A 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 438 through 443 removed outlier: 3.569A pdb=" N THR 3 443 " --> pdb=" O GLY 3 439 " (cutoff:3.500A) Processing helix chain '3' and resid 460 through 465 removed outlier: 3.736A pdb=" N ALA 3 465 " --> pdb=" O ALA 3 461 " (cutoff:3.500A) Processing helix chain '3' and resid 475 through 478 Processing helix chain '3' and resid 479 through 493 removed outlier: 3.765A pdb=" N VAL 3 484 " --> pdb=" O ASP 3 480 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 533 Processing helix chain '3' and resid 536 through 541 Processing helix chain '3' and resid 554 through 570 Processing helix chain '3' and resid 652 through 667 removed outlier: 3.707A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL 3 667 " --> pdb=" O ALA 3 663 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 688 removed outlier: 3.614A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 716 removed outlier: 4.165A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 3.624A pdb=" N ALA 3 726 " --> pdb=" O ASN 3 722 " (cutoff:3.500A) Processing helix chain '4' and resid 188 through 200 removed outlier: 4.085A 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: 4.040A pdb=" N LEU 4 257 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 removed outlier: 3.666A pdb=" N VAL 4 268 " --> pdb=" O TYR 4 264 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL 4 281 " --> pdb=" O LYS 4 277 " (cutoff:3.500A) Processing helix chain '4' and resid 318 through 322 removed outlier: 3.575A pdb=" N ILE 4 322 " --> pdb=" O PRO 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 402 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 removed outlier: 3.623A pdb=" N VAL 4 512 " --> pdb=" O LYS 4 508 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 526 removed outlier: 3.522A pdb=" N LEU 4 521 " --> pdb=" O ASP 4 517 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE 4 526 " --> pdb=" O LEU 4 522 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 removed outlier: 3.803A pdb=" N ILE 4 577 " --> pdb=" O SER 4 573 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) removed outlier: 3.519A 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 650 removed outlier: 3.733A pdb=" N SER 4 643 " --> pdb=" O ASP 4 639 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU 4 650 " --> pdb=" O HIS 4 646 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 removed outlier: 4.091A 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: 3.787A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.795A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) removed outlier: 3.515A 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: 4.081A 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: 3.859A 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: 3.869A 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 421 through 433 removed outlier: 3.934A pdb=" N LEU 5 425 " --> pdb=" O ALA 5 421 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU 5 426 " --> pdb=" O LYS 5 422 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS 5 427 " --> pdb=" O SER 5 423 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE 5 428 " --> pdb=" O GLN 5 424 " (cutoff:3.500A) Processing helix chain '5' and resid 469 through 473 Processing helix chain '5' and resid 486 through 491 removed outlier: 3.806A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) Processing helix chain '5' and resid 492 through 499 removed outlier: 3.963A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 550 removed outlier: 3.826A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 3.736A 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 576 through 590 removed outlier: 4.041A pdb=" N ASN 5 581 " --> pdb=" O THR 5 577 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA 5 582 " --> pdb=" O GLY 5 578 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN 5 587 " --> pdb=" O MET 5 583 " (cutoff:3.500A) removed outlier: 3.714A 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: 3.533A pdb=" N GLU 5 639 " --> pdb=" O ILE 5 635 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 667 removed outlier: 3.558A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 690 removed outlier: 3.662A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) Processing helix chain '5' and resid 708 through 722 removed outlier: 3.613A pdb=" N LEU 5 718 " --> pdb=" O PHE 5 714 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS 5 719 " --> pdb=" O GLU 5 715 " (cutoff:3.500A) Processing helix chain '5' and resid 730 through 740 Processing helix chain '5' and resid 742 through 758 removed outlier: 3.985A pdb=" N LEU 5 746 " --> pdb=" O ARG 5 742 " (cutoff:3.500A) removed outlier: 3.843A 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: 4.004A 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 172 Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 275 through 279 Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 501 through 507 removed outlier: 3.768A pdb=" N SER 6 507 " --> pdb=" O VAL 6 503 " (cutoff:3.500A) Processing helix chain '6' and resid 509 through 521 removed outlier: 3.548A pdb=" N LEU 6 516 " --> pdb=" O GLU 6 512 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 530 Processing helix chain '6' and resid 531 through 533 No H-bonds generated for 'chain '6' and resid 531 through 533' Processing helix chain '6' and resid 540 through 553 removed outlier: 3.717A pdb=" N LYS 6 544 " --> pdb=" O HIS 6 540 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS 6 545 " --> pdb=" O GLU 6 541 " (cutoff:3.500A) Processing helix chain '6' and resid 581 through 592 removed outlier: 3.841A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 626 through 631 Processing helix chain '6' and resid 640 through 644 removed outlier: 3.847A pdb=" N LYS 6 643 " --> pdb=" O GLU 6 640 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET 6 644 " --> pdb=" O PHE 6 641 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 640 through 644' Processing helix chain '6' and resid 645 through 659 removed outlier: 4.490A pdb=" N HIS 6 653 " --> pdb=" O GLN 6 649 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) removed outlier: 4.639A 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: 3.615A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE 6 709 " --> pdb=" O ILE 6 705 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 736 removed outlier: 3.653A pdb=" N THR 6 725 " --> pdb=" O GLU 6 721 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU 6 726 " --> pdb=" O LYS 6 722 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 759 Processing helix chain '6' and resid 766 through 786 removed outlier: 3.626A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 814 removed outlier: 3.837A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 840 removed outlier: 3.600A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 28 removed outlier: 3.829A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 3.541A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (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 removed outlier: 3.579A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 154 removed outlier: 3.970A pdb=" N ARG 7 152 " --> pdb=" O LEU 7 148 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 193 through 198 removed outlier: 3.815A pdb=" N THR 7 197 " --> pdb=" O PRO 7 193 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 215 removed outlier: 3.892A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 231 through 235 removed outlier: 3.529A pdb=" N PHE 7 234 " --> pdb=" O LYS 7 231 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU 7 235 " --> pdb=" O GLY 7 232 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 231 through 235' Processing helix chain '7' and resid 286 through 291 Processing helix chain '7' and resid 388 through 392 removed outlier: 3.931A 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 418 Processing helix chain '7' and resid 425 through 438 removed outlier: 3.551A pdb=" N GLY 7 438 " --> pdb=" O LEU 7 434 " (cutoff:3.500A) Processing helix chain '7' and resid 444 through 448 removed outlier: 3.776A pdb=" N GLY 7 447 " --> pdb=" O VAL 7 444 " (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 582 Processing helix chain '7' and resid 587 through 594 removed outlier: 3.911A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 4.432A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 649 removed outlier: 3.865A pdb=" N ALA 7 643 " --> pdb=" O ARG 7 639 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG 7 649 " --> pdb=" O ALA 7 645 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 655 No H-bonds generated for 'chain '7' and resid 653 through 655' Processing helix chain '7' and resid 656 through 672 Processing helix chain '7' and resid 673 through 677 Processing helix chain '7' and resid 685 through 703 removed outlier: 3.958A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 726 removed outlier: 3.556A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.598A 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: 4.989A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 96 through 101 removed outlier: 4.251A pdb=" N ILE C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 3.530A 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: 3.868A pdb=" N ALA C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 167 removed outlier: 4.295A pdb=" N SER C 163 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 192 removed outlier: 3.720A pdb=" N ILE C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.629A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 112 removed outlier: 3.788A pdb=" N MET D 84 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 154 removed outlier: 3.799A 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: 3.683A 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 203 through 207 removed outlier: 3.673A pdb=" N GLN D 207 " --> pdb=" O GLU D 204 " (cutoff:3.500A) 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 20 Processing helix chain 'E' and resid 35 through 52 removed outlier: 3.629A 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 131 through 136 Processing helix chain 'E' and resid 150 through 153 removed outlier: 3.803A pdb=" N GLY E 153 " --> pdb=" O ASP E 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 150 through 153' Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.755A pdb=" N ALA E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.728A pdb=" N ILE E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 284 through 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: 3.785A pdb=" N LYS E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 381 through 396 removed outlier: 5.223A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.486A 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 Processing helix chain 'E' and resid 489 through 517 removed outlier: 3.686A pdb=" N ARG E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 512 " --> pdb=" O ASN E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 540 removed outlier: 3.831A 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 634 through 647 removed outlier: 4.757A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'F' and resid 13 through 27 removed outlier: 3.510A pdb=" N LEU F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.676A 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 removed outlier: 3.503A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 195 through 200 Processing helix chain 'F' and resid 211 through 231 removed outlier: 4.258A pdb=" N VAL F 215 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE F 218 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 removed outlier: 3.796A pdb=" N LEU F 275 " --> pdb=" O LYS F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 358 removed outlier: 3.687A pdb=" N THR F 358 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 4.365A pdb=" N LYS F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE F 385 " --> pdb=" O LYS F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 426 removed outlier: 3.616A pdb=" N MET F 414 " --> pdb=" O ASP F 410 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 469 removed outlier: 3.676A pdb=" N PHE F 462 " --> pdb=" O PHE F 458 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA F 464 " --> pdb=" O ASN F 460 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU F 465 " --> pdb=" O ASN F 461 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 466 " --> pdb=" O PHE F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 489 through 497 removed outlier: 3.985A 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 removed outlier: 3.516A pdb=" N HIS F 553 " --> pdb=" O ARG F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 610 removed outlier: 4.066A pdb=" N THR F 599 " --> pdb=" O LYS F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 631 removed outlier: 3.844A 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 Processing helix chain 'G' and resid 1524 through 1539 Processing helix chain 'G' and resid 1539 through 1547 Processing helix chain 'G' and resid 1568 through 1570 No H-bonds generated for 'chain 'G' and resid 1568 through 1570' Processing helix chain 'G' and resid 1571 through 1582 removed outlier: 3.893A 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: 3.841A pdb=" N ASN G1608 " --> pdb=" O ARG G1605 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET G1610 " --> pdb=" O LEU G1607 " (cutoff:3.500A) Processing helix chain 'G' and resid 1626 through 1657 removed outlier: 4.154A pdb=" N THR G1630 " --> pdb=" O ASN G1626 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY G1643 " --> pdb=" O VAL G1639 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N SER G1644 " --> pdb=" O LEU G1640 " (cutoff:3.500A) Processing helix chain 'G' and resid 1659 through 1663 Processing helix chain 'G' and resid 1667 through 1683 removed outlier: 4.044A pdb=" N ILE G1671 " --> pdb=" O SER G1667 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE G1672 " --> pdb=" O MET G1668 " (cutoff:3.500A) Processing helix chain 'G' and resid 1700 through 1704 Processing helix chain 'G' and resid 1706 through 1714 Processing helix chain 'G' and resid 1738 through 1747 Processing helix chain 'G' and resid 1784 through 1804 removed outlier: 3.605A pdb=" N LYS G1804 " --> pdb=" O ASP G1800 " (cutoff:3.500A) Processing helix chain 'G' and resid 1806 through 1822 removed outlier: 4.346A pdb=" N ALA G1817 " --> pdb=" O VAL G1813 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER G1818 " --> pdb=" O ASN G1814 " (cutoff:3.500A) Processing helix chain 'G' and resid 1829 through 1854 removed outlier: 4.043A 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: 3.633A 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 removed outlier: 3.586A pdb=" N MET G1958 " --> pdb=" O GLU G1954 " (cutoff:3.500A) Processing helix chain 'G' and resid 2003 through 2006 Processing helix chain 'G' and resid 2007 through 2026 Processing helix chain 'G' and resid 2049 through 2064 removed outlier: 3.775A pdb=" N GLU G2053 " --> pdb=" O ASN G2049 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET G2062 " --> pdb=" O LEU G2058 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU G2064 " --> pdb=" O HIS G2060 " (cutoff:3.500A) Processing helix chain 'G' and resid 2068 through 2083 removed outlier: 3.774A pdb=" N ILE G2082 " --> pdb=" O GLU G2078 " (cutoff:3.500A) removed outlier: 4.064A 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: 3.659A pdb=" N LEU G2142 " --> pdb=" O ASN G2138 " (cutoff:3.500A) Processing helix chain 'G' and resid 2190 through 2208 removed outlier: 3.869A 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: 3.637A pdb=" N ASN H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 61 removed outlier: 3.552A pdb=" N ILE H 37 " --> pdb=" O HIS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 104 removed outlier: 3.538A pdb=" N LEU H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN H 103 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN H 104 " --> pdb=" O MET H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 142 removed outlier: 3.680A pdb=" N LYS H 142 " --> pdb=" O ILE H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 203 Processing helix chain 'I' and resid 12 through 22 Processing helix chain 'I' and resid 56 through 62 removed outlier: 4.284A pdb=" N LEU I 60 " --> pdb=" O ASP I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 82 removed outlier: 3.512A pdb=" N GLN I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 108 removed outlier: 3.772A pdb=" N ARG I 100 " --> pdb=" O LYS I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 129 Processing helix chain 'I' and resid 137 through 160 removed outlier: 3.561A pdb=" N LEU I 141 " --> pdb=" O PRO I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 199 removed outlier: 3.500A pdb=" N LEU I 181 " --> pdb=" O GLU I 177 " (cutoff:3.500A) Proline residue: I 183 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 244 Processing sheet with id=AA2, first strand: chain '2' and resid 331 through 334 removed outlier: 3.547A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU 2 407 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG 2 458 " --> pdb=" O GLU 2 423 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLU 2 423 " --> pdb=" O ARG 2 458 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (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: 6.288A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA 2 566 " --> pdb=" O ASP 2 607 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY 2 543 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.812A 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 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: 3.863A pdb=" N GLU 3 183 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS 3 178 " --> pdb=" O PHE 3 298 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE 3 298 " --> pdb=" O LYS 3 178 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG 3 291 " --> pdb=" O PRO 3 328 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN 3 293 " --> pdb=" O VAL 3 326 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL 3 326 " --> pdb=" O ASN 3 293 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL 3 295 " --> pdb=" O ASN 3 324 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS 3 318 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N THR 3 319 " --> pdb=" O SER 3 273 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASP 3 275 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE 3 321 " --> pdb=" O ASP 3 275 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP 3 279 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR 3 325 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU 3 278 " --> pdb=" O GLN 3 254 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN 3 254 " --> pdb=" O LEU 3 278 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG 3 255 " --> pdb=" O THR 3 189 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N THR 3 189 " --> pdb=" O ARG 3 255 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR 3 257 " --> pdb=" O THR 3 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 242 through 243 removed outlier: 5.480A pdb=" N LEU 3 196 " --> pdb=" O ILE 3 251 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE 3 251 " --> pdb=" O LEU 3 196 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG 3 198 " --> pdb=" O THR 3 249 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 242 through 243 removed outlier: 3.951A 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 Processing sheet with id=AB4, first strand: chain '3' and resid 429 through 433 removed outlier: 3.564A pdb=" N ALA 3 515 " --> pdb=" O ILE 3 472 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.365A 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: 7.164A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N TYR 4 306 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 6.615A 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: 4.792A pdb=" N LYS 4 329 " --> pdb=" O LYS 4 312 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 311 through 312 removed outlier: 4.792A pdb=" N LYS 4 329 " --> pdb=" O LYS 4 312 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS 4 465 " --> pdb=" O THR 4 436 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE 4 442 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THR 4 459 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N SER 4 414 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N VAL 4 461 " --> pdb=" O SER 4 414 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER 4 416 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL 4 463 " --> pdb=" O SER 4 416 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS 4 418 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N HIS 4 465 " --> pdb=" O CYS 4 418 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N TYR 4 420 " --> pdb=" O HIS 4 465 " (cutoff:3.500A) removed outlier: 12.836A pdb=" N LYS 4 467 " --> pdb=" O TYR 4 420 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AC2, first strand: chain '4' and resid 590 through 592 removed outlier: 3.554A pdb=" N ASP 4 632 " --> pdb=" O THR 4 591 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN 4 563 " --> pdb=" O LEU 4 704 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N TYR 4 706 " --> pdb=" O ASN 4 563 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 604 through 607 removed outlier: 3.748A pdb=" N GLU 4 617 " --> pdb=" O TYR 4 604 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL 4 615 " --> pdb=" O THR 4 606 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC5, first strand: chain '5' and resid 60 through 64 Processing sheet with id=AC6, first strand: chain '5' and resid 189 through 193 removed outlier: 8.171A pdb=" N SER 5 174 " --> pdb=" O PHE 5 250 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N PHE 5 250 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ALA 5 176 " --> pdb=" O SER 5 248 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N SER 5 248 " --> pdb=" O ALA 5 176 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N TYR 5 178 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLU 5 246 " --> pdb=" O TYR 5 178 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE 5 330 " --> pdb=" O THR 5 275 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR 5 277 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLY 5 332 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 10.599A pdb=" N ASP 5 279 " --> pdb=" O GLY 5 332 " (cutoff:3.500A) removed outlier: 13.059A pdb=" N GLN 5 334 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 398 through 399 removed outlier: 4.129A pdb=" N LYS 5 398 " --> pdb=" O LEU 5 406 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU 5 406 " --> pdb=" O LYS 5 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '5' and resid 436 through 440 removed outlier: 6.506A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 451 through 455 Processing sheet with id=AD1, first strand: chain '5' and resid 501 through 506 Processing sheet with id=AD2, first strand: chain '5' and resid 727 through 729 removed outlier: 3.678A pdb=" N THR 5 728 " --> pdb=" O ILE 5 770 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN 5 769 " --> pdb=" O ARG 5 764 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG 5 764 " --> pdb=" O ASN 5 769 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 150 through 154 Processing sheet with id=AD4, first strand: chain '6' and resid 317 through 322 removed outlier: 5.813A pdb=" N ALA 6 307 " --> pdb=" O ASN 6 320 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU 6 322 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N TYR 6 305 " --> pdb=" O GLU 6 322 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 317 through 322 removed outlier: 5.813A pdb=" N ALA 6 307 " --> pdb=" O ASN 6 320 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU 6 322 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N TYR 6 305 " --> pdb=" O GLU 6 322 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '6' and resid 301 through 311 current: chain '6' and resid 450 through 461 removed outlier: 5.406A pdb=" N ILE 6 452 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL 6 404 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 402 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE 6 402 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA 6 456 " --> pdb=" O VAL 6 400 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL 6 400 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG 6 296 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '6' and resid 596 through 599 removed outlier: 3.649A pdb=" N GLY 6 575 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 610 through 613 Processing sheet with id=AD8, first strand: chain '6' and resid 660 through 665 Processing sheet with id=AD9, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AE1, first strand: chain '7' and resid 270 through 272 removed outlier: 8.294A pdb=" N PHE 7 307 " --> pdb=" O PRO 7 253 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N VAL 7 255 " --> pdb=" O SER 7 305 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N SER 7 305 " --> pdb=" O VAL 7 255 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N VAL 7 257 " --> pdb=" O ARG 7 303 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ARG 7 303 " --> pdb=" O VAL 7 257 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N SER 7 330 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N LEU 7 376 " --> pdb=" O SER 7 330 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN 7 332 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA 7 378 " --> pdb=" O ASN 7 332 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N HIS 7 334 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N PHE 7 380 " --> pdb=" O HIS 7 334 " (cutoff:3.500A) removed outlier: 11.054A pdb=" N ASN 7 336 " --> pdb=" O PHE 7 380 " (cutoff:3.500A) removed outlier: 13.604A pdb=" N ARG 7 382 " --> pdb=" O ASN 7 336 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR 7 352 " --> pdb=" O GLN 7 379 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL 7 381 " --> pdb=" O ASP 7 350 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP 7 350 " --> pdb=" O VAL 7 381 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY 7 243 " --> pdb=" O VAL 7 349 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR 7 246 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL 7 248 " --> pdb=" O GLU 7 312 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLU 7 312 " --> pdb=" O VAL 7 248 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 480 through 483 removed outlier: 6.198A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP 7 517 " --> pdb=" O ARG 7 560 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N SER 7 562 " --> pdb=" O ASP 7 517 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY 7 519 " --> pdb=" O SER 7 562 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU 7 564 " --> pdb=" O GLY 7 519 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY 7 460 " --> pdb=" O ALA 7 567 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N MET 7 600 " --> pdb=" O CYS 7 457 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET 7 459 " --> pdb=" O MET 7 600 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 43 through 47 Processing sheet with id=AE4, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.742A pdb=" N ILE D 274 " --> pdb=" O LEU I 170 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 247 through 249 removed outlier: 3.854A pdb=" N ASN D 249 " --> pdb=" O LYS D 253 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.579A pdb=" N LEU E 81 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU E 123 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU E 83 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU E 27 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL E 59 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER E 56 " --> pdb=" O PHE H 190 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 316 through 324 Processing sheet with id=AE8, first strand: chain 'E' and resid 520 through 521 removed outlier: 6.867A pdb=" N ARG E 526 " --> pdb=" O VAL E 568 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ALA E 570 " --> pdb=" O ARG E 526 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N CYS E 528 " --> pdb=" O ALA E 570 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N ILE E 572 " --> pdb=" O CYS E 528 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 580 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 171 through 174 removed outlier: 6.190A pdb=" N GLU F 538 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL F 640 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL F 540 " --> pdb=" O VAL F 640 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS F 642 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE F 542 " --> pdb=" O CYS F 642 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 181 through 184 removed outlier: 3.500A pdb=" N GLN F 189 " --> pdb=" O ASN F 184 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.878A pdb=" N ILE F 313 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU F 329 " --> pdb=" O THR F 342 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N MET F 344 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU F 327 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 326 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY F 286 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP F 296 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE F 339 " --> pdb=" O GLU F 306 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 523 through 525 removed outlier: 4.485A pdb=" N PHE F 399 " --> pdb=" O TYR F 675 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR F 675 " --> pdb=" O PHE F 399 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 523 through 525 removed outlier: 4.485A pdb=" N PHE F 399 " --> pdb=" O TYR F 675 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR F 675 " --> pdb=" O PHE F 399 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 1444 through 1445 removed outlier: 6.150A pdb=" N VAL G1324 " --> pdb=" O THR G1341 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR G1341 " --> pdb=" O VAL G1324 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N PHE G1463 " --> pdb=" O ASN G1348 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR G1350 " --> pdb=" O PHE G1463 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 1375 through 1378 removed outlier: 3.642A pdb=" N LEU G1375 " --> pdb=" O THR G1401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR G1401 " --> pdb=" O LEU G1375 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR G1358 " --> pdb=" O VAL G1426 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL G1426 " --> pdb=" O TYR G1358 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS G1360 " --> pdb=" O LEU G1424 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 1500 through 1501 removed outlier: 5.545A pdb=" N LEU G1590 " --> pdb=" O VAL G1613 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 1725 through 1727 removed outlier: 6.847A pdb=" N ASP G1733 " --> pdb=" O LYS G1903 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR G1905 " --> pdb=" O VAL G1731 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL G1731 " --> pdb=" O TYR G1905 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN G1865 " --> pdb=" O ALA G1861 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA G1861 " --> pdb=" O GLN G1865 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU G1867 " --> pdb=" O VAL G1859 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 1725 through 1727 removed outlier: 6.658A pdb=" N LEU G1920 " --> pdb=" O ASP G1907 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU G1909 " --> pdb=" O SER G1918 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER G1918 " --> pdb=" O LEU G1909 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP G1911 " --> pdb=" O ASN G1916 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ASN G1916 " --> pdb=" O TRP G1911 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 2102 through 2107 removed outlier: 6.637A pdb=" N ILE G2117 " --> pdb=" O PRO G2104 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 2162 through 2163 Processing sheet with id=AG3, first strand: chain 'H' and resid 173 through 176 removed outlier: 3.572A pdb=" N GLY H 179 " --> pdb=" O THR H 176 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 24 through 27 removed outlier: 3.526A pdb=" N THR I 69 " --> pdb=" O ILE I 27 " (cutoff:3.500A) 2377 hydrogen bonds defined for protein. 6801 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: 30.39 Time building geometry restraints manager: 14.76 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: 17466 1.34 - 1.46: 11068 1.46 - 1.58: 25041 1.58 - 1.70: 37 1.70 - 1.82: 385 Bond restraints: 53997 Sorted by residual: bond pdb=" CB PRO I 4 " pdb=" CG PRO I 4 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.91e+00 bond pdb=" CA PRO D 116 " pdb=" C PRO D 116 " ideal model delta sigma weight residual 1.514 1.507 0.007 5.50e-03 3.31e+04 1.78e+00 bond pdb=" C LEU I 3 " pdb=" N PRO I 4 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" C PRO E 128 " pdb=" N TRP E 129 " ideal model delta sigma weight residual 1.327 1.338 -0.010 9.40e-03 1.13e+04 1.20e+00 bond pdb=" CG LEU 5 763 " pdb=" CD2 LEU 5 763 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 ... (remaining 53992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 72297 2.14 - 4.28: 702 4.28 - 6.41: 90 6.41 - 8.55: 13 8.55 - 10.69: 4 Bond angle restraints: 73106 Sorted by residual: angle pdb=" C ALA G1393 " pdb=" CA ALA G1393 " pdb=" CB ALA G1393 " ideal model delta sigma weight residual 116.54 110.57 5.97 1.15e+00 7.56e-01 2.69e+01 angle pdb=" C GLY 7 445 " pdb=" N ASP 7 446 " pdb=" CA ASP 7 446 " ideal model delta sigma weight residual 121.54 128.48 -6.94 1.91e+00 2.74e-01 1.32e+01 angle pdb=" CA ALA G1393 " pdb=" C ALA G1393 " pdb=" N GLY G1394 " ideal model delta sigma weight residual 119.52 116.81 2.71 7.90e-01 1.60e+00 1.17e+01 angle pdb=" C TRP I 119 " pdb=" N LEU I 120 " pdb=" CA LEU I 120 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C SER 7 677 " pdb=" N LYS 7 678 " pdb=" CA LYS 7 678 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 ... (remaining 73101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.16: 31862 29.16 - 58.32: 1121 58.32 - 87.48: 103 87.48 - 116.64: 7 116.64 - 145.80: 1 Dihedral angle restraints: 33094 sinusoidal: 13666 harmonic: 19428 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 300.00 154.20 145.80 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C4' ADP 61101 " pdb=" C5' ADP 61101 " pdb=" O5' ADP 61101 " pdb=" PA ADP 61101 " ideal model delta sinusoidal sigma weight residual -180.00 -90.86 -89.14 1 2.00e+01 2.50e-03 2.36e+01 dihedral pdb=" CA CYS 6 311 " pdb=" C CYS 6 311 " pdb=" N ASP 6 312 " pdb=" CA ASP 6 312 " ideal model delta harmonic sigma weight residual 180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 33091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 6316 0.043 - 0.085: 1530 0.085 - 0.128: 527 0.128 - 0.171: 19 0.171 - 0.213: 3 Chirality restraints: 8395 Sorted by residual: chirality pdb=" CG LEU 2 814 " pdb=" CB LEU 2 814 " pdb=" CD1 LEU 2 814 " pdb=" CD2 LEU 2 814 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASP 7 446 " pdb=" N ASP 7 446 " pdb=" C ASP 7 446 " pdb=" CB ASP 7 446 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.07e-01 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 2.54 0.18 2.00e-01 2.50e+01 8.34e-01 ... (remaining 8392 not shown) Planarity restraints: 9312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 3 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO I 4 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO I 4 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO I 4 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 120 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.45e+00 pdb=" C LEU I 120 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU I 120 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL I 121 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 129 " -0.011 2.00e-02 2.50e+03 1.57e-02 6.17e+00 pdb=" CG TRP E 129 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP E 129 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 129 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 129 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 129 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 129 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 129 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 129 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 129 " -0.001 2.00e-02 2.50e+03 ... (remaining 9309 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 301 2.54 - 3.13: 40501 3.13 - 3.72: 80828 3.72 - 4.31: 105095 4.31 - 4.90: 177752 Nonbonded interactions: 404477 Sorted by model distance: nonbonded pdb="MG MG 31001 " pdb=" O3B ATP 31002 " model vdw 1.945 2.170 nonbonded pdb=" O1G ATP 7 901 " pdb="MG MG 7 902 " model vdw 2.003 2.170 nonbonded pdb=" O1B ATP 7 901 " pdb="MG MG 7 902 " model vdw 2.007 2.170 nonbonded pdb="MG MG 31001 " pdb=" O1A ATP 31002 " model vdw 2.020 2.170 nonbonded pdb="MG MG 31001 " pdb=" O2G ATP 31002 " model vdw 2.053 2.170 ... (remaining 404472 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: 4.220 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: 0.040 Extract box with map and model: 2.010 Check model and map are aligned: 0.370 Set scattering table: 0.420 Process input model: 125.020 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.190 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 53997 Z= 0.157 Angle : 0.536 10.689 73106 Z= 0.275 Chirality : 0.041 0.213 8395 Planarity : 0.004 0.106 9312 Dihedral : 14.336 145.797 20472 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 6529 helix: 1.20 (0.10), residues: 2634 sheet: 0.11 (0.16), residues: 1027 loop : -0.91 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 129 HIS 0.008 0.001 HIS E 126 PHE 0.032 0.001 PHE 6 118 TYR 0.022 0.001 TYR G1881 ARG 0.006 0.000 ARG 5 764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 6.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 616 ASP cc_start: 0.7759 (m-30) cc_final: 0.7368 (m-30) REVERT: 4 607 ARG cc_start: 0.7608 (tpt90) cc_final: 0.7269 (tpt90) REVERT: 5 752 LEU cc_start: 0.7782 (pp) cc_final: 0.7314 (pp) REVERT: 6 393 ASP cc_start: 0.8574 (m-30) cc_final: 0.8302 (m-30) REVERT: 6 519 MET cc_start: 0.7674 (ptt) cc_final: 0.7359 (ptt) REVERT: 6 701 MET cc_start: 0.7778 (ppp) cc_final: 0.7394 (ppp) REVERT: 7 402 MET cc_start: 0.7878 (mmm) cc_final: 0.7661 (tpt) REVERT: 7 621 MET cc_start: 0.8566 (tmm) cc_final: 0.8145 (tmm) REVERT: 7 638 MET cc_start: 0.8477 (mpp) cc_final: 0.8104 (mpp) REVERT: 7 652 MET cc_start: 0.5288 (tmm) cc_final: 0.3895 (ppp) REVERT: C 79 MET cc_start: 0.8273 (mmp) cc_final: 0.8016 (mtm) REVERT: F 55 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6970 (tm-30) REVERT: F 188 MET cc_start: 0.7590 (mpp) cc_final: 0.6952 (tmm) REVERT: G 1899 ASP cc_start: 0.7937 (t70) cc_final: 0.7660 (t0) REVERT: H 62 MET cc_start: 0.7925 (pmm) cc_final: 0.7626 (pmm) REVERT: I 66 MET cc_start: 0.7344 (mmt) cc_final: 0.7059 (mmt) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.5997 time to fit residues: 329.2063 Evaluate side-chains 236 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 6.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 554 optimal weight: 20.0000 chunk 497 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 335 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 514 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 313 optimal weight: 4.9990 chunk 383 optimal weight: 0.1980 chunk 596 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 405 HIS 2 442 ASN C 130 GLN E 269 ASN F 186 HIS ** G1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 53997 Z= 0.201 Angle : 0.574 11.868 73106 Z= 0.299 Chirality : 0.042 0.184 8395 Planarity : 0.004 0.102 9312 Dihedral : 7.858 146.513 7465 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 0.39 % Allowed : 5.73 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.11), residues: 6529 helix: 1.24 (0.10), residues: 2740 sheet: 0.01 (0.16), residues: 1006 loop : -0.92 (0.12), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G1798 HIS 0.004 0.001 HIS 2 809 PHE 0.022 0.001 PHE D 251 TYR 0.027 0.001 TYR G1881 ARG 0.003 0.000 ARG 3 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 6.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 352 PHE cc_start: 0.7075 (p90) cc_final: 0.6820 (p90) REVERT: 2 616 ASP cc_start: 0.7977 (m-30) cc_final: 0.7571 (m-30) REVERT: 4 199 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7446 (ptp) REVERT: 4 637 MET cc_start: 0.8324 (tpp) cc_final: 0.7993 (tmm) REVERT: 4 777 MET cc_start: 0.8223 (ptt) cc_final: 0.7983 (mtm) REVERT: 4 811 MET cc_start: 0.7960 (pmm) cc_final: 0.7391 (pmm) REVERT: 5 485 MET cc_start: 0.7782 (ttt) cc_final: 0.7547 (ttp) REVERT: 5 583 MET cc_start: 0.6943 (tmm) cc_final: 0.6357 (ptt) REVERT: 5 689 MET cc_start: 0.6861 (mmm) cc_final: 0.6497 (tpt) REVERT: 6 143 MET cc_start: 0.8100 (mtm) cc_final: 0.7700 (mtm) REVERT: 6 701 MET cc_start: 0.7628 (ppp) cc_final: 0.7364 (ppp) REVERT: 7 402 MET cc_start: 0.7881 (mmm) cc_final: 0.7680 (tpt) REVERT: 7 448 MET cc_start: 0.5390 (tpt) cc_final: 0.4953 (mtm) REVERT: 7 621 MET cc_start: 0.8624 (tmm) cc_final: 0.8221 (tmm) REVERT: 7 638 MET cc_start: 0.8525 (mpp) cc_final: 0.8130 (mpp) REVERT: C 8 ASP cc_start: 0.7744 (t70) cc_final: 0.7455 (t70) REVERT: D 129 MET cc_start: 0.8461 (mpp) cc_final: 0.8250 (mpp) REVERT: F 55 GLN cc_start: 0.7278 (tm-30) cc_final: 0.7037 (tm-30) REVERT: F 70 TRP cc_start: 0.5865 (t-100) cc_final: 0.5593 (t-100) REVERT: F 91 MET cc_start: 0.4002 (mmt) cc_final: 0.3775 (mmt) REVERT: F 188 MET cc_start: 0.7539 (mpp) cc_final: 0.7022 (tmm) REVERT: G 1465 MET cc_start: 0.8665 (tmm) cc_final: 0.7537 (mmm) REVERT: G 1899 ASP cc_start: 0.7890 (t70) cc_final: 0.7585 (t0) REVERT: I 66 MET cc_start: 0.7353 (mmt) cc_final: 0.7085 (mmt) outliers start: 23 outliers final: 13 residues processed: 259 average time/residue: 0.6227 time to fit residues: 281.7531 Evaluate side-chains 240 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 6.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 733 LEU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 5 residue 533 LEU Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 642 GLU Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 2211 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 331 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 496 optimal weight: 0.9980 chunk 406 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 597 optimal weight: 2.9990 chunk 645 optimal weight: 2.9990 chunk 532 optimal weight: 10.0000 chunk 592 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 479 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 442 ASN 2 551 GLN 3 340 GLN ** 7 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 53997 Z= 0.221 Angle : 0.565 12.946 73106 Z= 0.293 Chirality : 0.042 0.185 8395 Planarity : 0.004 0.099 9312 Dihedral : 7.822 145.485 7465 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 0.84 % Allowed : 9.29 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.10), residues: 6529 helix: 1.22 (0.10), residues: 2765 sheet: -0.09 (0.16), residues: 1007 loop : -0.97 (0.12), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 240 HIS 0.005 0.001 HIS 5 188 PHE 0.021 0.001 PHE 6 118 TYR 0.021 0.001 TYR E 399 ARG 0.006 0.000 ARG E 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 6.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7235 (p90) REVERT: 2 616 ASP cc_start: 0.7931 (m-30) cc_final: 0.7489 (m-30) REVERT: 4 199 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7489 (ptp) REVERT: 4 811 MET cc_start: 0.8166 (pmm) cc_final: 0.7385 (pmm) REVERT: 5 583 MET cc_start: 0.6771 (tmm) cc_final: 0.6044 (ptp) REVERT: 6 519 MET cc_start: 0.7568 (ptt) cc_final: 0.6966 (ptt) REVERT: 6 629 MET cc_start: 0.8768 (mmm) cc_final: 0.8391 (tpp) REVERT: 6 701 MET cc_start: 0.7596 (ppp) cc_final: 0.7275 (ppp) REVERT: 7 66 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7410 (mpp) REVERT: 7 444 VAL cc_start: 0.4200 (OUTLIER) cc_final: 0.3886 (p) REVERT: 7 448 MET cc_start: 0.5503 (tpt) cc_final: 0.4943 (mtm) REVERT: 7 638 MET cc_start: 0.8600 (mpp) cc_final: 0.8257 (mpp) REVERT: C 8 ASP cc_start: 0.7816 (t70) cc_final: 0.7578 (t70) REVERT: C 79 MET cc_start: 0.8322 (mmp) cc_final: 0.7948 (mtm) REVERT: D 129 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8154 (mpp) REVERT: D 206 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8397 (pp) REVERT: F 70 TRP cc_start: 0.5553 (t-100) cc_final: 0.5352 (t-100) REVERT: F 91 MET cc_start: 0.4095 (mmt) cc_final: 0.3827 (mmt) REVERT: F 188 MET cc_start: 0.7572 (mpp) cc_final: 0.6965 (tmm) REVERT: G 1798 TRP cc_start: 0.7517 (m-10) cc_final: 0.7316 (m-10) REVERT: G 1899 ASP cc_start: 0.7882 (t70) cc_final: 0.7571 (t0) REVERT: G 2211 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7654 (p0) REVERT: I 66 MET cc_start: 0.7344 (mmt) cc_final: 0.7086 (mmt) REVERT: I 148 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8542 (mt) outliers start: 49 outliers final: 20 residues processed: 275 average time/residue: 0.6107 time to fit residues: 296.9505 Evaluate side-chains 249 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 6.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 3 residue 733 LEU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 5 residue 429 VAL Chi-restraints excluded: chain 5 residue 533 LEU Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 444 VAL Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 2211 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 148 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 590 optimal weight: 1.9990 chunk 449 optimal weight: 1.9990 chunk 310 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 401 optimal weight: 0.9990 chunk 599 optimal weight: 0.7980 chunk 635 optimal weight: 0.6980 chunk 313 optimal weight: 4.9990 chunk 568 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 398 HIS 3 532 ASN E 126 HIS F 55 GLN ** F 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 53997 Z= 0.140 Angle : 0.518 12.290 73106 Z= 0.267 Chirality : 0.041 0.180 8395 Planarity : 0.004 0.098 9312 Dihedral : 7.637 143.946 7465 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 0.89 % Allowed : 10.91 % Favored : 88.21 % 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: 0.32 (0.11), residues: 6529 helix: 1.40 (0.10), residues: 2765 sheet: -0.01 (0.16), residues: 997 loop : -0.91 (0.12), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 119 HIS 0.004 0.001 HIS 5 188 PHE 0.020 0.001 PHE 6 118 TYR 0.031 0.001 TYR 3 576 ARG 0.005 0.000 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 6.523 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: 2 352 PHE cc_start: 0.7249 (p90) cc_final: 0.6971 (p90) REVERT: 2 385 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7077 (p90) REVERT: 2 616 ASP cc_start: 0.7956 (m-30) cc_final: 0.7523 (m-30) REVERT: 4 199 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7450 (ptp) REVERT: 4 280 MET cc_start: 0.6757 (mmp) cc_final: 0.6461 (mmm) REVERT: 4 607 ARG cc_start: 0.7818 (tpt90) cc_final: 0.7506 (tpt90) REVERT: 4 811 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7529 (pmm) REVERT: 5 575 ILE cc_start: 0.7476 (tp) cc_final: 0.7254 (tt) REVERT: 5 583 MET cc_start: 0.6785 (tmm) cc_final: 0.6123 (ptp) REVERT: 5 689 MET cc_start: 0.6810 (mmm) cc_final: 0.6604 (tpt) REVERT: 6 519 MET cc_start: 0.7505 (ptt) cc_final: 0.6998 (ptt) REVERT: 6 629 MET cc_start: 0.8708 (mmm) cc_final: 0.8388 (tpp) REVERT: 7 66 MET cc_start: 0.7544 (mpp) cc_final: 0.7257 (mpp) REVERT: 7 402 MET cc_start: 0.6204 (tpt) cc_final: 0.5660 (mmt) REVERT: 7 448 MET cc_start: 0.5348 (tpt) cc_final: 0.4932 (mtm) REVERT: 7 529 MET cc_start: 0.7175 (ptp) cc_final: 0.6853 (ptp) REVERT: 7 621 MET cc_start: 0.8684 (tmm) cc_final: 0.8392 (tmm) REVERT: 7 638 MET cc_start: 0.8542 (mpp) cc_final: 0.8229 (mpp) REVERT: C 8 ASP cc_start: 0.7815 (t70) cc_final: 0.7581 (t70) REVERT: D 129 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8081 (mpp) REVERT: D 206 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8469 (pp) REVERT: E 362 MET cc_start: 0.7059 (mmp) cc_final: 0.6853 (mmp) REVERT: E 380 MET cc_start: 0.8821 (tmm) cc_final: 0.8594 (tmm) REVERT: E 539 TYR cc_start: 0.7253 (m-80) cc_final: 0.6839 (m-80) REVERT: F 91 MET cc_start: 0.3973 (mmt) cc_final: 0.3737 (mmt) REVERT: F 188 MET cc_start: 0.7585 (mpp) cc_final: 0.7058 (tmm) REVERT: F 673 MET cc_start: 0.7885 (tmm) cc_final: 0.7619 (tmm) REVERT: G 1465 MET cc_start: 0.8609 (tmm) cc_final: 0.7407 (mmm) REVERT: G 1798 TRP cc_start: 0.7547 (m-10) cc_final: 0.6755 (m-10) REVERT: G 1899 ASP cc_start: 0.7895 (t70) cc_final: 0.7605 (t0) REVERT: G 2211 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7615 (p0) REVERT: I 66 MET cc_start: 0.7317 (mmt) cc_final: 0.7055 (mmt) outliers start: 52 outliers final: 21 residues processed: 292 average time/residue: 0.5963 time to fit residues: 307.2289 Evaluate side-chains 252 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 6.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 733 LEU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 4 residue 646 HIS Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 752 LEU Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 679 PHE Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 2211 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 528 optimal weight: 9.9990 chunk 360 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 472 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 541 optimal weight: 0.9990 chunk 438 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 570 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN 3 330 HIS 7 585 ASN 7 683 GLN F 340 HIS ** G1593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 53997 Z= 0.206 Angle : 0.554 12.800 73106 Z= 0.284 Chirality : 0.042 0.185 8395 Planarity : 0.004 0.095 9312 Dihedral : 7.666 141.997 7465 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 1.16 % Allowed : 12.15 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 6529 helix: 1.39 (0.10), residues: 2765 sheet: -0.08 (0.16), residues: 995 loop : -0.93 (0.12), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 70 HIS 0.005 0.001 HIS 5 188 PHE 0.020 0.001 PHE 6 118 TYR 0.017 0.001 TYR G1881 ARG 0.004 0.000 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 6.385 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: 2 352 PHE cc_start: 0.7260 (p90) cc_final: 0.7013 (p90) REVERT: 2 385 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7093 (p90) REVERT: 2 567 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8496 (m) REVERT: 2 616 ASP cc_start: 0.7950 (m-30) cc_final: 0.7511 (m-30) REVERT: 4 199 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7475 (ptp) REVERT: 4 811 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7394 (pmm) REVERT: 5 485 MET cc_start: 0.7830 (ttt) cc_final: 0.7436 (ttp) REVERT: 5 575 ILE cc_start: 0.7600 (tp) cc_final: 0.7369 (tt) REVERT: 5 583 MET cc_start: 0.6775 (tmm) cc_final: 0.6079 (ptp) REVERT: 6 519 MET cc_start: 0.7546 (ptt) cc_final: 0.7049 (ptt) REVERT: 6 629 MET cc_start: 0.8752 (mmm) cc_final: 0.8431 (tpp) REVERT: 7 66 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7322 (mpp) REVERT: 7 638 MET cc_start: 0.8664 (mpp) cc_final: 0.8335 (mpp) REVERT: C 8 ASP cc_start: 0.7923 (t70) cc_final: 0.7702 (t70) REVERT: D 129 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8083 (mpp) REVERT: D 206 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8561 (pp) REVERT: E 380 MET cc_start: 0.8861 (tmm) cc_final: 0.7919 (tmm) REVERT: E 539 TYR cc_start: 0.7336 (m-80) cc_final: 0.6921 (m-80) REVERT: F 70 TRP cc_start: 0.5995 (t-100) cc_final: 0.5791 (t-100) REVERT: F 91 MET cc_start: 0.4115 (mmt) cc_final: 0.3776 (mmt) REVERT: F 188 MET cc_start: 0.7669 (mpp) cc_final: 0.7093 (tmm) REVERT: F 494 MET cc_start: 0.8490 (tmm) cc_final: 0.8271 (tpt) REVERT: F 673 MET cc_start: 0.7931 (tmm) cc_final: 0.7652 (tmm) REVERT: G 1465 MET cc_start: 0.8621 (tmm) cc_final: 0.7394 (mmm) REVERT: G 1713 MET cc_start: 0.8730 (tpp) cc_final: 0.8502 (mmm) REVERT: G 1798 TRP cc_start: 0.7638 (m-10) cc_final: 0.6815 (m-10) REVERT: G 1899 ASP cc_start: 0.7930 (t70) cc_final: 0.7635 (t0) REVERT: I 66 MET cc_start: 0.7281 (mmt) cc_final: 0.7033 (mmt) outliers start: 68 outliers final: 38 residues processed: 288 average time/residue: 0.5954 time to fit residues: 303.3775 Evaluate side-chains 265 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 6.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 3 residue 100 LEU Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 733 LEU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 533 LEU Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 642 GLU Chi-restraints excluded: chain 5 residue 752 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 515 LEU Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 679 PHE Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 213 optimal weight: 5.9990 chunk 571 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 372 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 635 optimal weight: 0.9990 chunk 527 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 333 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 779 HIS 5 196 ASN ** F 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 53997 Z= 0.148 Angle : 0.526 12.315 73106 Z= 0.268 Chirality : 0.041 0.180 8395 Planarity : 0.004 0.094 9312 Dihedral : 7.554 141.094 7465 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 0.99 % Allowed : 13.29 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.11), residues: 6529 helix: 1.50 (0.10), residues: 2757 sheet: -0.00 (0.16), residues: 988 loop : -0.88 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 119 HIS 0.004 0.001 HIS 5 188 PHE 0.017 0.001 PHE F 62 TYR 0.016 0.001 TYR G1881 ARG 0.004 0.000 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 6.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 352 PHE cc_start: 0.7224 (p90) cc_final: 0.6995 (p90) REVERT: 2 385 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7110 (p90) REVERT: 2 616 ASP cc_start: 0.7964 (m-30) cc_final: 0.7527 (m-30) REVERT: 4 199 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7369 (ptp) REVERT: 4 280 MET cc_start: 0.6507 (mmp) cc_final: 0.5971 (mmm) REVERT: 4 607 ARG cc_start: 0.7652 (tpt90) cc_final: 0.7354 (tpt90) REVERT: 4 777 MET cc_start: 0.8023 (mtm) cc_final: 0.7533 (mtm) REVERT: 4 780 MET cc_start: 0.8074 (ppp) cc_final: 0.7559 (ppp) REVERT: 4 811 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7380 (pmm) REVERT: 5 575 ILE cc_start: 0.7472 (tp) cc_final: 0.7264 (tt) REVERT: 5 583 MET cc_start: 0.6756 (tmm) cc_final: 0.6032 (ptp) REVERT: 5 689 MET cc_start: 0.6948 (mmm) cc_final: 0.6648 (tpt) REVERT: 5 763 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8627 (mt) REVERT: 6 629 MET cc_start: 0.8702 (mmm) cc_final: 0.8402 (tpp) REVERT: 7 66 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7359 (mpp) REVERT: 7 621 MET cc_start: 0.8680 (tmm) cc_final: 0.8410 (tmm) REVERT: 7 638 MET cc_start: 0.8565 (mpp) cc_final: 0.8266 (mpp) REVERT: D 129 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8027 (mpp) REVERT: D 206 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8566 (pp) REVERT: E 362 MET cc_start: 0.7291 (mmp) cc_final: 0.7013 (mmp) REVERT: E 380 MET cc_start: 0.8890 (tmm) cc_final: 0.7918 (tmm) REVERT: E 539 TYR cc_start: 0.7255 (m-80) cc_final: 0.6834 (m-80) REVERT: F 70 TRP cc_start: 0.5710 (t-100) cc_final: 0.5504 (t-100) REVERT: F 91 MET cc_start: 0.3840 (mmt) cc_final: 0.3625 (mmp) REVERT: F 188 MET cc_start: 0.7656 (mpp) cc_final: 0.7069 (tmm) REVERT: F 673 MET cc_start: 0.7929 (tmm) cc_final: 0.7286 (tmm) REVERT: G 1537 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: G 1798 TRP cc_start: 0.7589 (m-10) cc_final: 0.6947 (m-10) REVERT: I 66 MET cc_start: 0.7336 (mmt) cc_final: 0.7094 (mmt) outliers start: 58 outliers final: 42 residues processed: 281 average time/residue: 0.5858 time to fit residues: 293.7052 Evaluate side-chains 271 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 6.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 733 LEU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 4 residue 361 ASP Chi-restraints excluded: chain 4 residue 646 HIS Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 642 GLU Chi-restraints excluded: chain 5 residue 752 LEU Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 547 ILE Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 515 LEU Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 679 PHE Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 116 PHE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 2211 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 612 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 362 optimal weight: 5.9990 chunk 464 optimal weight: 1.9990 chunk 359 optimal weight: 9.9990 chunk 535 optimal weight: 8.9990 chunk 354 optimal weight: 20.0000 chunk 633 optimal weight: 0.0270 chunk 396 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 chunk 292 optimal weight: 0.7980 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 253 GLN 4 683 ASN 7 112 HIS 7 145 GLN ** F 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 53997 Z= 0.281 Angle : 0.607 13.131 73106 Z= 0.311 Chirality : 0.043 0.186 8395 Planarity : 0.004 0.092 9312 Dihedral : 7.755 142.086 7465 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 1.48 % Allowed : 13.87 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 6529 helix: 1.26 (0.10), residues: 2758 sheet: -0.16 (0.16), residues: 985 loop : -1.02 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 240 HIS 0.005 0.001 HIS 3 374 PHE 0.018 0.002 PHE 6 118 TYR 0.020 0.002 TYR E 399 ARG 0.004 0.000 ARG 4 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 226 time to evaluate : 6.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7296 (p90) REVERT: 2 567 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8545 (m) REVERT: 2 616 ASP cc_start: 0.7949 (m-30) cc_final: 0.7484 (m-30) REVERT: 2 783 MET cc_start: 0.7918 (tpp) cc_final: 0.6889 (tmm) REVERT: 4 199 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7392 (ptp) REVERT: 4 280 MET cc_start: 0.6638 (mmp) cc_final: 0.6185 (mmm) REVERT: 4 356 MET cc_start: 0.7093 (ptp) cc_final: 0.6565 (ptp) REVERT: 4 607 ARG cc_start: 0.7827 (tpt90) cc_final: 0.7544 (tpt90) REVERT: 4 777 MET cc_start: 0.8142 (mtm) cc_final: 0.7452 (mtm) REVERT: 4 780 MET cc_start: 0.8193 (ppp) cc_final: 0.7517 (ppp) REVERT: 4 811 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7388 (pmm) REVERT: 5 172 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8995 (pp) REVERT: 5 575 ILE cc_start: 0.7858 (tp) cc_final: 0.7580 (tt) REVERT: 5 583 MET cc_start: 0.6860 (tmm) cc_final: 0.6158 (ptp) REVERT: 5 763 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8541 (mt) REVERT: 6 629 MET cc_start: 0.8763 (mmm) cc_final: 0.8460 (tpp) REVERT: 7 66 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7492 (mpp) REVERT: 7 448 MET cc_start: 0.5266 (tpt) cc_final: 0.4669 (mtm) REVERT: 7 529 MET cc_start: 0.6876 (ptp) cc_final: 0.6543 (ptp) REVERT: 7 638 MET cc_start: 0.8685 (mpp) cc_final: 0.8379 (mpp) REVERT: D 129 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: D 206 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8573 (pp) REVERT: E 362 MET cc_start: 0.7451 (mmp) cc_final: 0.7230 (mmp) REVERT: E 380 MET cc_start: 0.8886 (tmm) cc_final: 0.7935 (tmm) REVERT: F 188 MET cc_start: 0.7561 (mpp) cc_final: 0.6943 (tmm) REVERT: G 1465 MET cc_start: 0.8626 (tmm) cc_final: 0.7422 (mmm) REVERT: G 1537 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: G 1798 TRP cc_start: 0.7703 (m-10) cc_final: 0.6832 (m-10) REVERT: I 66 MET cc_start: 0.7327 (mmt) cc_final: 0.7079 (mmt) outliers start: 87 outliers final: 55 residues processed: 301 average time/residue: 0.5857 time to fit residues: 315.2456 Evaluate side-chains 286 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 6.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 100 LEU Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 660 VAL Chi-restraints excluded: chain 3 residue 733 LEU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 4 residue 646 HIS Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 533 LEU Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 642 GLU Chi-restraints excluded: chain 5 residue 752 LEU Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 547 ILE Chi-restraints excluded: chain 7 residue 64 MET Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 515 LEU Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 679 PHE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 116 PHE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1402 LEU Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 2039 VAL Chi-restraints excluded: chain G residue 2181 CYS Chi-restraints excluded: chain G residue 2211 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 32 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 391 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 378 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 402 optimal weight: 0.4980 chunk 431 optimal weight: 4.9990 chunk 313 optimal weight: 0.0870 chunk 59 optimal weight: 0.9980 chunk 497 optimal weight: 0.1980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 688 ASN 3 691 ASN 4 253 GLN 4 683 ASN 7 697 GLN F 55 GLN ** F 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 53997 Z= 0.133 Angle : 0.534 12.094 73106 Z= 0.270 Chirality : 0.041 0.176 8395 Planarity : 0.004 0.091 9312 Dihedral : 7.451 140.196 7465 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 1.06 % Allowed : 14.60 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 6529 helix: 1.48 (0.10), residues: 2758 sheet: -0.02 (0.16), residues: 985 loop : -0.90 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP F 70 HIS 0.003 0.001 HIS 3 712 PHE 0.024 0.001 PHE F 62 TYR 0.018 0.001 TYR 7 411 ARG 0.004 0.000 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 246 time to evaluate : 6.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 352 PHE cc_start: 0.7328 (p90) cc_final: 0.7035 (p90) REVERT: 2 385 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7183 (p90) REVERT: 2 616 ASP cc_start: 0.7929 (m-30) cc_final: 0.7471 (m-30) REVERT: 2 764 MET cc_start: 0.8466 (mmt) cc_final: 0.8228 (mmt) REVERT: 2 783 MET cc_start: 0.7757 (tpp) cc_final: 0.6821 (tmm) REVERT: 4 199 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7318 (ptp) REVERT: 4 280 MET cc_start: 0.6549 (mmp) cc_final: 0.6108 (mmm) REVERT: 4 356 MET cc_start: 0.6730 (ptp) cc_final: 0.6186 (ptp) REVERT: 4 607 ARG cc_start: 0.7801 (tpt90) cc_final: 0.7484 (tpt90) REVERT: 4 777 MET cc_start: 0.8056 (mtm) cc_final: 0.7404 (mtm) REVERT: 4 780 MET cc_start: 0.8092 (ppp) cc_final: 0.7464 (ppp) REVERT: 4 811 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7515 (pmm) REVERT: 5 65 MET cc_start: 0.7661 (tpp) cc_final: 0.7392 (tpp) REVERT: 5 575 ILE cc_start: 0.7428 (tp) cc_final: 0.7211 (tt) REVERT: 5 583 MET cc_start: 0.6704 (tmm) cc_final: 0.6049 (ptp) REVERT: 5 689 MET cc_start: 0.6916 (mmm) cc_final: 0.6611 (tpt) REVERT: 5 763 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8580 (mt) REVERT: 6 629 MET cc_start: 0.8620 (mmm) cc_final: 0.8321 (tpp) REVERT: 7 66 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7428 (mpp) REVERT: 7 448 MET cc_start: 0.5297 (tpt) cc_final: 0.4672 (mtm) REVERT: 7 506 MET cc_start: 0.4234 (mmp) cc_final: 0.3981 (mmm) REVERT: 7 529 MET cc_start: 0.6812 (ptp) cc_final: 0.6510 (ptp) REVERT: 7 638 MET cc_start: 0.8516 (mpp) cc_final: 0.8264 (mpp) REVERT: D 206 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8567 (pp) REVERT: E 362 MET cc_start: 0.7289 (mmp) cc_final: 0.6785 (mmt) REVERT: E 539 TYR cc_start: 0.7217 (m-80) cc_final: 0.6768 (m-80) REVERT: F 188 MET cc_start: 0.7640 (mpp) cc_final: 0.7053 (tmm) REVERT: F 494 MET cc_start: 0.8514 (tmm) cc_final: 0.7926 (tmm) REVERT: G 1465 MET cc_start: 0.8393 (tmm) cc_final: 0.7278 (mmm) REVERT: G 1798 TRP cc_start: 0.7572 (m-10) cc_final: 0.6686 (m-10) REVERT: I 66 MET cc_start: 0.7352 (mmt) cc_final: 0.7126 (mmt) outliers start: 62 outliers final: 46 residues processed: 297 average time/residue: 0.5947 time to fit residues: 312.8115 Evaluate side-chains 285 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 5.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 100 LEU Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 4 residue 646 HIS Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 642 GLU Chi-restraints excluded: chain 5 residue 752 LEU Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 515 LEU Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 679 PHE Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 116 PHE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1402 LEU Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 2039 VAL Chi-restraints excluded: chain G residue 2211 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 32 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 576 optimal weight: 10.0000 chunk 606 optimal weight: 0.4980 chunk 553 optimal weight: 9.9990 chunk 590 optimal weight: 5.9990 chunk 355 optimal weight: 0.0770 chunk 257 optimal weight: 10.0000 chunk 463 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 533 optimal weight: 10.0000 chunk 558 optimal weight: 8.9990 chunk 588 optimal weight: 2.9990 overall best weight: 2.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 239 ASN 4 253 GLN 4 683 ASN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 53997 Z= 0.260 Angle : 0.600 12.921 73106 Z= 0.306 Chirality : 0.042 0.186 8395 Planarity : 0.004 0.089 9312 Dihedral : 7.602 140.952 7465 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 1.19 % Allowed : 14.78 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.11), residues: 6529 helix: 1.33 (0.10), residues: 2758 sheet: -0.09 (0.17), residues: 970 loop : -0.99 (0.12), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP F 70 HIS 0.005 0.001 HIS 3 201 PHE 0.024 0.002 PHE F 62 TYR 0.019 0.002 TYR E 399 ARG 0.004 0.000 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 232 time to evaluate : 6.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7219 (p90) REVERT: 2 616 ASP cc_start: 0.7965 (m-30) cc_final: 0.7493 (m-30) REVERT: 2 783 MET cc_start: 0.7879 (tpp) cc_final: 0.6879 (tmm) REVERT: 4 199 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7342 (ptp) REVERT: 4 280 MET cc_start: 0.6791 (mmp) cc_final: 0.6367 (mmm) REVERT: 4 356 MET cc_start: 0.6906 (ptp) cc_final: 0.6342 (ptp) REVERT: 4 777 MET cc_start: 0.8212 (mtm) cc_final: 0.7776 (mtm) REVERT: 4 780 MET cc_start: 0.8294 (ppp) cc_final: 0.7663 (ppp) REVERT: 4 811 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7335 (pmm) REVERT: 5 172 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9005 (pp) REVERT: 5 404 MET cc_start: 0.7818 (ptm) cc_final: 0.7611 (ptp) REVERT: 5 575 ILE cc_start: 0.7828 (tp) cc_final: 0.7549 (tt) REVERT: 5 583 MET cc_start: 0.6805 (tmm) cc_final: 0.6062 (ptp) REVERT: 5 763 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8685 (mt) REVERT: 6 629 MET cc_start: 0.8744 (mmm) cc_final: 0.8437 (tpp) REVERT: 7 66 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7571 (mpp) REVERT: 7 448 MET cc_start: 0.5564 (tpt) cc_final: 0.4828 (mtm) REVERT: 7 529 MET cc_start: 0.7087 (ptp) cc_final: 0.6519 (ptp) REVERT: 7 638 MET cc_start: 0.8659 (mpp) cc_final: 0.8384 (mpp) REVERT: D 129 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8078 (mpp) REVERT: E 539 TYR cc_start: 0.7416 (m-80) cc_final: 0.6948 (m-80) REVERT: F 188 MET cc_start: 0.7496 (mpp) cc_final: 0.6895 (tmm) REVERT: F 494 MET cc_start: 0.8604 (tmm) cc_final: 0.8018 (tmm) REVERT: F 673 MET cc_start: 0.7767 (tmm) cc_final: 0.7080 (tmm) REVERT: G 1439 MET cc_start: 0.9025 (mtt) cc_final: 0.8615 (mpp) REVERT: G 1465 MET cc_start: 0.8449 (tmm) cc_final: 0.7267 (mmm) REVERT: G 1537 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: G 1798 TRP cc_start: 0.7674 (m-10) cc_final: 0.6774 (m-10) REVERT: I 66 MET cc_start: 0.7344 (mmt) cc_final: 0.7090 (mmt) outliers start: 70 outliers final: 53 residues processed: 291 average time/residue: 0.5825 time to fit residues: 302.3460 Evaluate side-chains 290 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 229 time to evaluate : 6.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 100 LEU Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 660 VAL Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 4 residue 361 ASP Chi-restraints excluded: chain 4 residue 646 HIS Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 533 LEU Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 752 LEU Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 547 ILE Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 7 residue 64 MET Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 515 LEU Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 679 PHE Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 116 PHE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1402 LEU Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 1613 VAL Chi-restraints excluded: chain G residue 2039 VAL Chi-restraints excluded: chain G residue 2181 CYS Chi-restraints excluded: chain G residue 2211 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 387 optimal weight: 4.9990 chunk 623 optimal weight: 1.9990 chunk 380 optimal weight: 0.6980 chunk 296 optimal weight: 0.8980 chunk 433 optimal weight: 6.9990 chunk 654 optimal weight: 5.9990 chunk 602 optimal weight: 0.5980 chunk 521 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 402 optimal weight: 0.9990 chunk 319 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 253 GLN 4 683 ASN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 53997 Z= 0.143 Angle : 0.549 12.733 73106 Z= 0.274 Chirality : 0.041 0.176 8395 Planarity : 0.004 0.088 9312 Dihedral : 7.350 139.405 7465 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 0.95 % Allowed : 15.15 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 6529 helix: 1.49 (0.10), residues: 2765 sheet: 0.01 (0.16), residues: 987 loop : -0.92 (0.12), residues: 2777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP F 70 HIS 0.004 0.001 HIS G1835 PHE 0.028 0.001 PHE F 62 TYR 0.014 0.001 TYR G1881 ARG 0.003 0.000 ARG 5 734 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 6.768 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: 2 352 PHE cc_start: 0.7300 (p90) cc_final: 0.6959 (p90) REVERT: 2 385 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7205 (p90) REVERT: 2 577 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7838 (p) REVERT: 2 616 ASP cc_start: 0.7937 (m-30) cc_final: 0.7472 (m-30) REVERT: 2 764 MET cc_start: 0.8577 (mmt) cc_final: 0.8337 (mmt) REVERT: 2 783 MET cc_start: 0.7720 (tpp) cc_final: 0.6771 (tmm) REVERT: 4 199 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7271 (ptp) REVERT: 4 280 MET cc_start: 0.6765 (mmp) cc_final: 0.6332 (mmm) REVERT: 4 356 MET cc_start: 0.6725 (ptp) cc_final: 0.6499 (ptp) REVERT: 4 777 MET cc_start: 0.8185 (mtm) cc_final: 0.7791 (mtm) REVERT: 4 780 MET cc_start: 0.8168 (ppp) cc_final: 0.7584 (ppp) REVERT: 4 811 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7485 (pmm) REVERT: 5 575 ILE cc_start: 0.7499 (tp) cc_final: 0.7260 (tt) REVERT: 5 583 MET cc_start: 0.6704 (tmm) cc_final: 0.6051 (ptp) REVERT: 5 689 MET cc_start: 0.6923 (mmm) cc_final: 0.6612 (tpt) REVERT: 5 763 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8633 (mt) REVERT: 6 629 MET cc_start: 0.8619 (mmm) cc_final: 0.8313 (tpp) REVERT: 7 66 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7494 (mpp) REVERT: 7 448 MET cc_start: 0.5488 (tpt) cc_final: 0.4778 (mtm) REVERT: 7 506 MET cc_start: 0.4143 (mmp) cc_final: 0.3875 (mmm) REVERT: 7 529 MET cc_start: 0.6819 (ptp) cc_final: 0.6539 (ptp) REVERT: 7 638 MET cc_start: 0.8577 (mpp) cc_final: 0.8315 (mpp) REVERT: E 539 TYR cc_start: 0.7258 (m-80) cc_final: 0.6799 (m-80) REVERT: F 188 MET cc_start: 0.7638 (mpp) cc_final: 0.7051 (tmm) REVERT: F 494 MET cc_start: 0.8523 (tmm) cc_final: 0.7903 (tmm) REVERT: G 1439 MET cc_start: 0.9010 (mtt) cc_final: 0.8624 (mpp) REVERT: G 1465 MET cc_start: 0.8419 (tmm) cc_final: 0.7254 (mmm) REVERT: G 1798 TRP cc_start: 0.7547 (m-10) cc_final: 0.6675 (m-10) REVERT: I 66 MET cc_start: 0.7373 (mmt) cc_final: 0.7144 (mmt) outliers start: 56 outliers final: 47 residues processed: 292 average time/residue: 0.5920 time to fit residues: 310.6329 Evaluate side-chains 286 residues out of total 5944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 233 time to evaluate : 6.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 385 TYR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 577 THR Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 100 LEU Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 660 VAL Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 4 residue 361 ASP Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 576 HIS Chi-restraints excluded: chain 5 residue 752 LEU Chi-restraints excluded: chain 5 residue 763 LEU Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 797 VAL Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 515 LEU Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 679 PHE Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 116 PHE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 478 TRP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1537 GLU Chi-restraints excluded: chain G residue 1582 GLU Chi-restraints excluded: chain G residue 2039 VAL Chi-restraints excluded: chain G residue 2211 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain I residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 414 optimal weight: 4.9990 chunk 555 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 480 optimal weight: 9.9990 chunk 76 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 522 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 536 optimal weight: 10.0000 chunk 66 optimal weight: 0.0030 chunk 96 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 156 GLN C 130 GLN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.071403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058116 restraints weight = 265411.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.059484 restraints weight = 150147.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.060434 restraints weight = 101764.256| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 53997 Z= 0.134 Angle : 0.539 12.420 73106 Z= 0.268 Chirality : 0.041 0.179 8395 Planarity : 0.004 0.086 9312 Dihedral : 7.144 137.706 7465 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 0.99 % Allowed : 15.22 % Favored : 83.79 % 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: 0.50 (0.11), residues: 6529 helix: 1.60 (0.10), residues: 2755 sheet: 0.10 (0.16), residues: 988 loop : -0.85 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP F 70 HIS 0.004 0.000 HIS G1835 PHE 0.027 0.001 PHE F 62 TYR 0.016 0.001 TYR G1881 ARG 0.004 0.000 ARG I 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8313.04 seconds wall clock time: 206 minutes 56.09 seconds (12416.09 seconds total)