Starting phenix.real_space_refine on Mon Jun 24 12:55:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/06_2024/8p62_17458_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/06_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_17458/06_2024/8p62_17458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/06_2024/8p62_17458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/06_2024/8p62_17458_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p62_17458/06_2024/8p62_17458_updated.pdb" } 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 Residue "6 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 20.40, per 1000 atoms: 0.38 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.36 Conformation dependent library (CDL) restraints added in 7.0 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... running ksdssp... Secondary structure from input PDB file: 251 helices and 59 sheets defined 40.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.93 Creating SS restraints... Processing helix chain '2' and resid 183 through 186 Processing helix chain '2' and resid 194 through 198 Processing helix chain '2' and resid 201 through 217 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 226 through 237 Processing helix chain '2' and resid 246 through 251 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 265 through 282 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 286 through 288 No H-bonds generated for 'chain '2' and resid 286 through 288' Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 478 through 487 Processing helix chain '2' and resid 493 through 499 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 568 through 570 No H-bonds generated for 'chain '2' and resid 568 through 570' Processing helix chain '2' and resid 573 through 576 No H-bonds generated for 'chain '2' and resid 573 through 576' Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 621 through 624 No H-bonds generated for 'chain '2' and resid 621 through 624' Processing helix chain '2' and resid 653 through 655 No H-bonds generated for 'chain '2' and resid 653 through 655' Processing helix chain '2' and resid 663 through 665 No H-bonds generated for 'chain '2' and resid 663 through 665' Processing helix chain '2' and resid 671 through 674 No H-bonds generated for 'chain '2' and resid 671 through 674' Processing helix chain '2' and resid 689 through 705 removed outlier: 3.606A pdb=" N GLU 2 693 " --> pdb=" O GLU 2 689 " (cutoff:3.500A) Processing helix chain '2' and resid 740 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 760 through 772 Processing helix chain '2' and resid 783 through 794 Processing helix chain '2' and resid 797 through 799 No H-bonds generated for 'chain '2' and resid 797 through 799' Processing helix chain '2' and resid 807 through 824 removed outlier: 3.923A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 848 removed outlier: 3.965A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) Processing helix chain '2' and resid 854 through 863 removed outlier: 3.663A pdb=" N ALA 2 862 " --> pdb=" O ARG 2 858 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) Processing helix chain '3' and resid 20 through 34 Processing helix chain '3' and resid 37 through 51 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 122 through 136 Processing helix chain '3' and resid 146 through 148 No H-bonds generated for 'chain '3' and resid 146 through 148' Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 344 through 354 Processing helix chain '3' and resid 359 through 366 Processing helix chain '3' and resid 375 through 385 Processing helix chain '3' and resid 416 through 425 Processing helix chain '3' and resid 439 through 443 removed outlier: 3.569A pdb=" N THR 3 443 " --> pdb=" O GLY 3 439 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 439 through 443' Processing helix chain '3' and resid 461 through 465 removed outlier: 3.736A pdb=" N ALA 3 465 " --> pdb=" O ALA 3 461 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 461 through 465' Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 492 removed outlier: 3.765A 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 529 through 532 No H-bonds generated for 'chain '3' and resid 529 through 532' Processing helix chain '3' and resid 537 through 540 No H-bonds generated for 'chain '3' and resid 537 through 540' Processing helix chain '3' and resid 555 through 569 Processing helix chain '3' and resid 653 through 666 removed outlier: 3.707A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) Processing helix chain '3' and resid 673 through 687 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 715 Processing helix chain '3' and resid 723 through 737 Processing helix chain '4' and resid 189 through 199 Processing helix chain '4' and resid 204 through 210 Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 254 through 263 Processing helix chain '4' and resid 265 through 284 removed outlier: 4.386A pdb=" N VAL 4 281 " --> pdb=" O LYS 4 277 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 403 through 405 No H-bonds generated for 'chain '4' and resid 403 through 405' Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 505 through 513 removed outlier: 3.627A pdb=" N ARG 4 510 " --> pdb=" O ALA 4 507 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU 4 511 " --> pdb=" O LYS 4 508 " (cutoff:3.500A) Processing helix chain '4' and resid 516 through 526 removed outlier: 4.397A pdb=" N TYR 4 519 " --> pdb=" O GLU 4 516 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU 4 521 " --> pdb=" O LEU 4 518 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE 4 526 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 574 through 584 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 620 through 624 Processing helix chain '4' and resid 640 through 649 removed outlier: 3.833A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 700 Processing helix chain '4' and resid 714 through 728 Processing helix chain '4' and resid 746 through 757 Processing helix chain '4' and resid 764 through 780 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 795 through 813 removed outlier: 5.648A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU 4 813 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) Processing helix chain '4' and resid 819 through 834 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) Processing helix chain '5' and resid 21 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 102 Proline residue: 5 88 - end of helix removed outlier: 3.859A pdb=" N THR 5 95 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) Processing helix chain '5' and resid 148 through 150 No H-bonds generated for 'chain '5' and resid 148 through 150' Processing helix chain '5' and resid 153 through 155 No H-bonds generated for 'chain '5' and resid 153 through 155' Processing helix chain '5' and resid 262 through 264 No H-bonds generated for 'chain '5' and resid 262 through 264' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 366 through 373 Processing helix chain '5' and resid 383 through 393 Processing helix chain '5' and resid 422 through 432 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 470 through 472 No H-bonds generated for 'chain '5' and resid 470 through 472' Processing helix chain '5' and resid 487 through 490 No H-bonds generated for 'chain '5' and resid 487 through 490' Processing helix chain '5' and resid 493 through 498 Processing helix chain '5' and resid 544 through 549 removed outlier: 3.826A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) Processing helix chain '5' and resid 563 through 575 Processing helix chain '5' and resid 580 through 589 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 596 through 609 Processing helix chain '5' and resid 616 through 640 removed outlier: 3.533A pdb=" N GLU 5 639 " --> pdb=" O ILE 5 635 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 667 removed outlier: 4.106A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 689 removed outlier: 3.662A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) Processing helix chain '5' and resid 709 through 721 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 739 Processing helix chain '5' and resid 743 through 757 removed outlier: 3.843A pdb=" N ASP 5 749 " --> pdb=" O GLN 5 745 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 121 Processing helix chain '6' and resid 135 through 146 Processing helix chain '6' and resid 155 through 159 Processing helix chain '6' and resid 163 through 165 No H-bonds generated for 'chain '6' and resid 163 through 165' Processing helix chain '6' and resid 167 through 171 Processing helix chain '6' and resid 174 through 192 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 197 No H-bonds generated for 'chain '6' and resid 194 through 197' Processing helix chain '6' and resid 276 through 278 No H-bonds generated for 'chain '6' and resid 276 through 278' Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 501 through 506 Processing helix chain '6' and resid 510 through 520 removed outlier: 3.548A pdb=" N LEU 6 516 " --> pdb=" O GLU 6 512 " (cutoff:3.500A) Processing helix chain '6' and resid 525 through 532 removed outlier: 4.182A pdb=" N ARG 6 531 " --> pdb=" O ASP 6 527 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 552 removed outlier: 3.568A pdb=" N LYS 6 545 " --> pdb=" O GLU 6 541 " (cutoff:3.500A) Processing helix chain '6' and resid 582 through 591 Processing helix chain '6' and resid 627 through 630 No H-bonds generated for 'chain '6' and resid 627 through 630' Processing helix chain '6' and resid 641 through 643 No H-bonds generated for 'chain '6' and resid 641 through 643' Processing helix chain '6' and resid 646 through 658 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 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 708 removed outlier: 3.615A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 735 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 748 through 760 removed outlier: 4.015A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 785 removed outlier: 3.626A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 813 Processing helix chain '6' and resid 821 through 839 Processing helix chain '7' and resid 14 through 27 Processing helix chain '7' and resid 62 through 71 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 92 Processing helix chain '7' and resid 103 through 108 Processing helix chain '7' and resid 111 through 123 removed outlier: 3.579A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 134 through 136 No H-bonds generated for 'chain '7' and resid 134 through 136' Processing helix chain '7' and resid 138 through 153 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 194 through 197 No H-bonds generated for 'chain '7' and resid 194 through 197' Processing helix chain '7' and resid 209 through 214 Processing helix chain '7' and resid 232 through 234 No H-bonds generated for 'chain '7' and resid 232 through 234' Processing helix chain '7' and resid 287 through 290 No H-bonds generated for 'chain '7' and resid 287 through 290' Processing helix chain '7' and resid 389 through 391 No H-bonds generated for 'chain '7' and resid 389 through 391' Processing helix chain '7' and resid 395 through 406 Processing helix chain '7' and resid 411 through 416 Processing helix chain '7' and resid 426 through 437 Processing helix chain '7' and resid 445 through 447 No H-bonds generated for 'chain '7' and resid 445 through 447' Processing helix chain '7' and resid 466 through 476 Processing helix chain '7' and resid 531 through 539 Processing helix chain '7' and resid 541 through 543 No H-bonds generated for 'chain '7' and resid 541 through 543' Processing helix chain '7' and resid 579 through 581 No H-bonds generated for 'chain '7' and resid 579 through 581' Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 606 through 622 removed outlier: 4.432A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 648 removed outlier: 3.865A pdb=" N ALA 7 643 " --> pdb=" O ARG 7 639 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 676 removed outlier: 4.875A pdb=" N ASP 7 658 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N MET 7 675 " --> pdb=" O LYS 7 672 " (cutoff:3.500A) Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 726 removed outlier: 3.598A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 removed outlier: 3.698A pdb=" N GLY C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.989A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 118 through 140 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 160 through 168 removed outlier: 3.784A pdb=" N LYS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 191 Processing helix chain 'D' and resid 56 through 72 removed outlier: 3.629A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 111 removed outlier: 3.644A pdb=" N ASN D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 153 Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 171 through 174 No H-bonds generated for 'chain 'D' and resid 171 through 174' Processing helix chain 'D' and resid 177 through 197 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 280 through 287 removed outlier: 4.094A pdb=" N ARG D 283 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP D 284 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 19 removed outlier: 4.549A pdb=" N SER E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 151 through 153 No H-bonds generated for 'chain 'E' and resid 151 through 153' Processing helix chain 'E' and resid 155 through 162 Processing helix chain 'E' and resid 224 through 240 removed outlier: 4.218A pdb=" N LYS E 227 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS E 228 " --> pdb=" O GLN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 267 through 280 removed outlier: 4.405A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 301 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 370 through 373 No H-bonds generated for 'chain 'E' and resid 370 through 373' Processing helix chain 'E' and resid 382 through 395 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 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 421 through 433 Processing helix chain 'E' and resid 463 through 484 removed outlier: 3.635A pdb=" N LEU E 484 " --> pdb=" O SER E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 516 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 536 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 542 through 557 Processing helix chain 'E' and resid 605 through 615 Processing helix chain 'E' and resid 634 through 646 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 14 through 26 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 35 through 48 Processing helix chain 'F' and resid 57 through 70 Processing helix chain 'F' and resid 81 through 93 Processing helix chain 'F' and resid 196 through 199 No H-bonds generated for 'chain 'F' and resid 196 through 199' Processing helix chain 'F' and resid 211 through 230 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 271 through 274 Processing helix chain 'F' and resid 352 through 359 removed outlier: 3.687A pdb=" N THR F 358 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE F 359 " --> pdb=" O THR F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 390 removed outlier: 4.244A pdb=" N ILE F 385 " --> pdb=" O LYS F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 425 Processing helix chain 'F' and resid 454 through 471 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) removed outlier: 3.550A pdb=" N SER F 470 " --> pdb=" O ALA F 466 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG F 471 " --> pdb=" O THR F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 478 Processing helix chain 'F' and resid 490 through 496 removed outlier: 3.985A pdb=" N VAL F 495 " --> pdb=" O TRP F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 512 No H-bonds generated for 'chain 'F' and resid 510 through 512' Processing helix chain 'F' and resid 516 through 519 No H-bonds generated for 'chain 'F' and resid 516 through 519' Processing helix chain 'F' and resid 547 through 552 Processing helix chain 'F' and resid 595 through 609 removed outlier: 3.789A pdb=" N THR F 599 " --> pdb=" O VAL F 596 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN F 609 " --> pdb=" O ILE F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 630 Processing helix chain 'G' and resid 1404 through 1410 Processing helix chain 'G' and resid 1433 through 1440 Processing helix chain 'G' and resid 1455 through 1460 Processing helix chain 'G' and resid 1524 through 1538 Processing helix chain 'G' and resid 1540 through 1546 Processing helix chain 'G' and resid 1569 through 1581 removed outlier: 3.535A pdb=" N ARG G1572 " --> pdb=" O LEU G1569 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU G1573 " --> pdb=" O TYR G1570 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER G1574 " --> pdb=" O ARG G1571 " (cutoff:3.500A) Processing helix chain 'G' and resid 1597 through 1603 Processing helix chain 'G' and resid 1605 through 1609 removed outlier: 3.841A pdb=" N ASN G1608 " --> pdb=" O ARG G1605 " (cutoff:3.500A) Processing helix chain 'G' and resid 1627 through 1656 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 1660 through 1662 No H-bonds generated for 'chain 'G' and resid 1660 through 1662' Processing helix chain 'G' and resid 1668 through 1682 removed outlier: 3.502A pdb=" N ILE G1672 " --> pdb=" O MET G1668 " (cutoff:3.500A) Processing helix chain 'G' and resid 1701 through 1703 No H-bonds generated for 'chain 'G' and resid 1701 through 1703' Processing helix chain 'G' and resid 1707 through 1713 Processing helix chain 'G' and resid 1739 through 1746 Processing helix chain 'G' and resid 1785 through 1803 Processing helix chain 'G' and resid 1807 through 1821 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 1830 through 1853 Processing helix chain 'G' and resid 1875 through 1877 No H-bonds generated for 'chain 'G' and resid 1875 through 1877' Processing helix chain 'G' and resid 1879 through 1891 Processing helix chain 'G' and resid 1893 through 1895 No H-bonds generated for 'chain 'G' and resid 1893 through 1895' Processing helix chain 'G' and resid 1940 through 1944 Processing helix chain 'G' and resid 1950 through 1974 removed outlier: 3.586A pdb=" N MET G1958 " --> pdb=" O GLU G1954 " (cutoff:3.500A) Processing helix chain 'G' and resid 2004 through 2006 No H-bonds generated for 'chain 'G' and resid 2004 through 2006' Processing helix chain 'G' and resid 2008 through 2025 Processing helix chain 'G' and resid 2050 through 2065 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) removed outlier: 4.989A pdb=" N SER G2065 " --> pdb=" O VAL G2061 " (cutoff:3.500A) Processing helix chain 'G' and resid 2069 through 2082 removed outlier: 3.774A pdb=" N ILE G2082 " --> pdb=" O GLU G2078 " (cutoff:3.500A) Processing helix chain 'G' and resid 2090 through 2092 No H-bonds generated for 'chain 'G' and resid 2090 through 2092' Processing helix chain 'G' and resid 2139 through 2158 Processing helix chain 'G' and resid 2191 through 2207 Processing helix chain 'G' and resid 2211 through 2218 Processing helix chain 'H' and resid 4 through 23 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 34 through 60 Processing helix chain 'H' and resid 65 through 103 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) Processing helix chain 'H' and resid 125 through 143 removed outlier: 3.680A pdb=" N LYS H 142 " --> pdb=" O ILE H 138 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 197 through 202 Processing helix chain 'I' and resid 13 through 21 Processing helix chain 'I' and resid 57 through 61 Processing helix chain 'I' and resid 73 through 81 Processing helix chain 'I' and resid 95 through 107 removed outlier: 3.772A pdb=" N ARG I 100 " --> pdb=" O LYS I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 138 through 161 removed outlier: 3.915A pdb=" N LYS I 161 " --> pdb=" O LEU I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 198 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= A, first strand: chain '2' and resid 241 through 244 removed outlier: 6.981A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL 2 244 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG 2 296 " --> pdb=" O VAL 2 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 406 through 410 removed outlier: 4.027A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN 2 391 " --> pdb=" O VAL 2 324 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL 2 324 " --> pdb=" O GLN 2 391 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 331 through 334 removed outlier: 3.547A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 525 through 527 Processing sheet with id= E, first strand: chain '2' and resid 679 through 683 removed outlier: 3.928A pdb=" N GLY 2 543 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY 2 602 " --> pdb=" O SER 2 645 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE 2 647 " --> pdb=" O GLY 2 602 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N ASN 2 651 " --> pdb=" O ILE 2 606 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 579 through 582 Processing sheet with id= G, first strand: chain '2' and resid 628 through 633 Processing sheet with id= H, first strand: chain '3' and resid 96 through 99 Processing sheet with id= I, first strand: chain '3' and resid 273 through 279 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: 3.811A pdb=" N LYS 3 188 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN 3 259 " --> pdb=" O VAL 3 186 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 259 " (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: 6.313A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 209 through 213 removed outlier: 6.681A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 391 through 393 Processing sheet with id= L, first strand: chain '3' and resid 545 through 549 removed outlier: 3.776A pdb=" N ILE 3 405 " --> pdb=" O VAL 3 512 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA 3 515 " --> pdb=" O ILE 3 472 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 444 through 448 Processing sheet with id= N, first strand: chain '3' and resid 494 through 499 Processing sheet with id= O, first strand: chain '4' and resid 241 through 244 Processing sheet with id= P, first strand: chain '4' and resid 414 through 420 removed outlier: 3.684A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (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) Processing sheet with id= Q, first strand: chain '4' and resid 354 through 359 removed outlier: 6.750A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 704 through 708 removed outlier: 6.441A pdb=" N ILE 4 671 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU 4 566 " --> pdb=" O ILE 4 671 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA 4 673 " --> pdb=" O LEU 4 566 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA 4 675 " --> pdb=" O GLY 4 568 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP 4 632 " --> pdb=" O THR 4 591 " (cutoff:3.500A) Processing sheet with id= S, 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= T, first strand: chain '4' and resid 653 through 658 Processing sheet with id= U, first strand: chain '5' and resid 60 through 64 removed outlier: 6.455A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain '5' and resid 273 through 279 removed outlier: 4.052A pdb=" N SER 5 168 " --> pdb=" O LYS 5 257 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN 5 259 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE 5 166 " --> pdb=" O GLN 5 259 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE 5 297 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE 5 330 " --> pdb=" O ILE 5 297 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER 5 299 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE 5 328 " --> pdb=" O SER 5 299 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR 5 301 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '5' and resid 189 through 193 removed outlier: 4.360A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 552 through 554 removed outlier: 6.896A pdb=" N GLY 5 475 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 475 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 451 through 455 Processing sheet with id= Z, first strand: chain '5' and resid 501 through 506 Processing sheet with id= AA, 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= AB, first strand: chain '5' and resid 173 through 178 removed outlier: 6.820A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '6' and resid 150 through 154 removed outlier: 6.480A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain '6' and resid 376 through 382 removed outlier: 3.696A pdb=" N GLN 6 357 " --> pdb=" O LEU 6 381 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG 6 296 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL 6 400 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA 6 456 " --> pdb=" O VAL 6 400 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE 6 402 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 402 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL 6 404 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE 6 452 " --> pdb=" O VAL 6 404 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '6' and resid 316 through 318 removed outlier: 3.555A pdb=" N ALA 6 316 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain '6' and resid 711 through 715 removed outlier: 3.649A pdb=" N GLY 6 575 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY 6 634 " --> pdb=" O SER 6 677 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU 6 679 " --> pdb=" O GLY 6 634 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 610 through 613 Processing sheet with id= AH, first strand: chain '6' and resid 660 through 665 Processing sheet with id= AI, first strand: chain '6' and resid 301 through 306 removed outlier: 6.995A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '7' and resid 77 through 81 removed outlier: 6.120A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain '7' and resid 330 through 336 removed outlier: 3.931A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY 7 243 " --> pdb=" O VAL 7 349 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 270 through 272 removed outlier: 4.739A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 596 through 600 removed outlier: 3.628A pdb=" N GLY 7 460 " --> pdb=" O ALA 7 567 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 252 through 257 removed outlier: 6.824A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 15 through 19 Processing sheet with id= AP, first strand: chain 'D' and resid 274 through 277 Processing sheet with id= AQ, first strand: chain 'D' and resid 255 through 260 Processing sheet with id= AR, first strand: chain 'E' and resid 57 through 61 removed outlier: 3.568A pdb=" N GLN E 57 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 31 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER E 80 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE E 30 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU E 82 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SER E 32 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL E 84 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP E 119 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU E 83 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR E 121 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 316 through 324 Processing sheet with id= AT, first strand: chain 'E' and resid 526 through 529 removed outlier: 3.527A pdb=" N LEU E 580 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP E 573 " --> pdb=" O THR E 578 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR E 578 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'F' and resid 171 through 174 removed outlier: 6.954A pdb=" N THR F 638 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N PHE F 542 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL F 640 " --> pdb=" O PHE F 542 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS F 657 " --> pdb=" O MET F 639 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU F 641 " --> pdb=" O LYS F 657 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE F 659 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing sheet with id= AV, 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= AW, first strand: chain 'F' and resid 281 through 286 removed outlier: 3.614A pdb=" N GLY F 286 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 326 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER F 343 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE F 331 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL F 341 " --> pdb=" O ILE F 331 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N PHE F 339 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU F 306 " --> pdb=" O PHE F 339 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL F 341 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP F 308 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N SER F 343 " --> pdb=" O ASP F 308 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP F 296 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'F' and resid 680 through 685 removed outlier: 3.745A pdb=" N TYR F 675 " --> pdb=" O PHE F 399 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE F 399 " --> pdb=" O TYR F 675 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU F 431 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR F 480 " --> pdb=" O LEU F 432 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N TRP F 434 " --> pdb=" O THR F 480 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE F 482 " --> pdb=" O TRP F 434 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'G' and resid 1346 through 1352 removed outlier: 6.490A pdb=" N THR G1341 " --> pdb=" O VAL G1324 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL G1324 " --> pdb=" O THR G1341 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'G' and resid 1355 through 1360 removed outlier: 3.531A pdb=" N THR G1401 " --> pdb=" O LEU G1375 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU G1375 " --> pdb=" O THR G1401 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'G' and resid 1484 through 1488 removed outlier: 6.369A pdb=" N LEU G1589 " --> pdb=" O GLY G1485 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU G1487 " --> pdb=" O LEU G1589 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU G1591 " --> pdb=" O LEU G1487 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU G1592 " --> pdb=" O VAL G1613 " (cutoff:3.500A) Processing sheet with id= BB, 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= BC, first strand: chain 'G' and resid 1899 through 1906 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: 3.776A pdb=" N TYR G1860 " --> pdb=" O LEU G1867 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS G1869 " --> pdb=" O ILE G1858 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE G1858 " --> pdb=" O LYS G1869 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'G' and resid 2106 through 2108 Processing sheet with id= BE, first strand: chain 'H' and resid 162 through 166 Processing sheet with id= BF, 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= BG, first strand: chain 'I' and resid 24 through 28 removed outlier: 3.526A pdb=" N THR I 69 " --> pdb=" O ILE I 27 " (cutoff:3.500A) 1983 hydrogen bonds defined for protein. 5517 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: 21.08 Time building geometry restraints manager: 18.16 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: 96.58 - 105.24: 1041 105.24 - 113.90: 31811 113.90 - 122.56: 33671 122.56 - 131.22: 6470 131.22 - 139.88: 113 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: 306 2.54 - 3.13: 40765 3.13 - 3.72: 81047 3.72 - 4.31: 105910 4.31 - 4.90: 177901 Nonbonded interactions: 405929 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 405924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 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: 0.050 Extract box with map and model: 14.530 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 116.640 Find NCS groups from input model: 2.180 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: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.070 ------------------------------------------------------------------------------- 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= 0.158 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 fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 4.678 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: 0.4788 time to fit residues: 262.0485 Evaluate side-chains 236 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 4.595 ------------------------------------------------------------------------------- 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: 1.9990 chunk 276 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 335 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 chunk 514 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 383 optimal weight: 0.9990 chunk 596 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 2 551 GLN ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 ASN ** 7 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 683 GLN C 130 GLN D 160 GLN E 269 ASN F 186 HIS F 236 GLN ** F 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 53997 Z= 0.269 Angle : 0.594 12.280 73106 Z= 0.307 Chirality : 0.043 0.189 8395 Planarity : 0.004 0.102 9312 Dihedral : 7.917 142.273 7465 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 0.56 % Allowed : 6.60 % Favored : 92.84 % 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: -0.03 (0.10), residues: 6529 helix: 1.04 (0.10), residues: 2677 sheet: -0.11 (0.16), residues: 1014 loop : -0.98 (0.12), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G1798 HIS 0.007 0.001 HIS 6 653 PHE 0.018 0.002 PHE 6 118 TYR 0.026 0.002 TYR G1881 ARG 0.004 0.000 ARG G1792 *********************** 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 268 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 4.625 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: 0.7252 (p90) cc_final: 0.7004 (p90) REVERT: 2 616 ASP cc_start: 0.7733 (m-30) cc_final: 0.7349 (m-30) REVERT: 4 811 MET cc_start: 0.8132 (pmm) cc_final: 0.7544 (pmm) REVERT: 5 485 MET cc_start: 0.7755 (ttt) cc_final: 0.7476 (ttp) REVERT: 6 701 MET cc_start: 0.7718 (ppp) cc_final: 0.7447 (ppp) REVERT: 7 153 MET cc_start: 0.8672 (tmm) cc_final: 0.8408 (tmm) REVERT: 7 402 MET cc_start: 0.7867 (mmm) cc_final: 0.7236 (tpt) REVERT: 7 529 MET cc_start: 0.7854 (ptp) cc_final: 0.7618 (ptp) REVERT: 7 621 MET cc_start: 0.8615 (tmm) cc_final: 0.8072 (tmm) REVERT: 7 638 MET cc_start: 0.8592 (mpp) cc_final: 0.8128 (mpp) REVERT: C 79 MET cc_start: 0.8313 (mmp) cc_final: 0.8020 (mtm) REVERT: E 362 MET cc_start: 0.7330 (mmp) cc_final: 0.7085 (mmp) REVERT: F 70 TRP cc_start: 0.5995 (t-100) cc_final: 0.5684 (t-100) REVERT: G 1465 MET cc_start: 0.8603 (tmm) cc_final: 0.7453 (mmm) REVERT: G 1886 MET cc_start: 0.8445 (tpp) cc_final: 0.8101 (tpp) REVERT: G 1899 ASP cc_start: 0.7947 (t70) cc_final: 0.7623 (t0) REVERT: G 2211 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7662 (p0) REVERT: I 63 MET cc_start: 0.8268 (ppp) cc_final: 0.8006 (ppp) REVERT: I 66 MET cc_start: 0.7340 (mmt) cc_final: 0.7075 (mmt) outliers start: 33 outliers final: 20 residues processed: 257 average time/residue: 0.4840 time to fit residues: 219.9637 Evaluate side-chains 244 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 223 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 3 residue 733 LEU Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 4 residue 728 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 355 ASP Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain C residue 7 ASP 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 136 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 331 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 496 optimal weight: 7.9990 chunk 406 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 597 optimal weight: 5.9990 chunk 645 optimal weight: 4.9990 chunk 532 optimal weight: 5.9990 chunk 592 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 479 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS E 269 ASN ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 53997 Z= 0.158 Angle : 0.510 12.177 73106 Z= 0.262 Chirality : 0.041 0.183 8395 Planarity : 0.004 0.100 9312 Dihedral : 7.672 138.369 7465 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 0.66 % Allowed : 9.95 % Favored : 89.38 % 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: 0.12 (0.11), residues: 6529 helix: 1.20 (0.10), residues: 2676 sheet: -0.07 (0.16), residues: 1015 loop : -0.92 (0.12), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 119 HIS 0.005 0.001 HIS 5 188 PHE 0.020 0.001 PHE 6 118 TYR 0.013 0.001 TYR 6 136 ARG 0.004 0.000 ARG H 38 *********************** 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 283 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 244 time to evaluate : 4.626 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: 0.7272 (p90) cc_final: 0.7050 (p90) REVERT: 2 616 ASP cc_start: 0.7771 (m-30) cc_final: 0.7396 (m-30) REVERT: 4 199 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7368 (ptp) REVERT: 4 565 LEU cc_start: 0.9193 (tp) cc_final: 0.8960 (tp) REVERT: 4 811 MET cc_start: 0.8198 (pmm) cc_final: 0.7323 (pmm) REVERT: 5 689 MET cc_start: 0.6895 (mmm) cc_final: 0.6538 (tpt) REVERT: 6 629 MET cc_start: 0.8672 (mmm) cc_final: 0.8289 (tpp) REVERT: 6 701 MET cc_start: 0.7595 (ppp) cc_final: 0.7317 (ppp) REVERT: 7 153 MET cc_start: 0.8608 (tmm) cc_final: 0.8379 (tmm) REVERT: 7 343 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8303 (pp) REVERT: 7 402 MET cc_start: 0.7702 (mmm) cc_final: 0.7187 (tpt) REVERT: 7 448 MET cc_start: 0.5455 (tpt) cc_final: 0.4905 (mtm) REVERT: 7 621 MET cc_start: 0.8510 (tmm) cc_final: 0.8112 (tmm) REVERT: 7 638 MET cc_start: 0.8600 (mpp) cc_final: 0.8265 (mpp) REVERT: D 129 MET cc_start: 0.8422 (mpp) cc_final: 0.8085 (mpp) REVERT: D 206 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7873 (pp) REVERT: F 188 MET cc_start: 0.7523 (mpp) cc_final: 0.6971 (tmm) REVERT: G 1465 MET cc_start: 0.8606 (tmm) cc_final: 0.7491 (mmm) REVERT: G 1899 ASP cc_start: 0.7941 (t70) cc_final: 0.7633 (t0) REVERT: G 2211 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7581 (p0) REVERT: I 63 MET cc_start: 0.8090 (ppp) cc_final: 0.7660 (ppp) REVERT: I 66 MET cc_start: 0.7333 (mmt) cc_final: 0.7078 (mmt) REVERT: I 148 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8483 (mt) outliers start: 39 outliers final: 20 residues processed: 271 average time/residue: 0.4942 time to fit residues: 235.6461 Evaluate side-chains 250 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 225 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 3 residue 410 ASP Chi-restraints excluded: chain 4 residue 199 MET Chi-restraints excluded: chain 4 residue 258 TYR Chi-restraints excluded: chain 4 residue 728 TYR Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 642 GLU Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 202 MET 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 G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR 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 H residue 182 ASN 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: 10.0000 chunk 449 optimal weight: 0.9980 chunk 310 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 401 optimal weight: 0.7980 chunk 599 optimal weight: 0.0040 chunk 635 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 568 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 340 GLN ** 7 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN ** 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 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 53997 Z= 0.173 Angle : 0.512 12.114 73106 Z= 0.262 Chirality : 0.041 0.184 8395 Planarity : 0.004 0.097 9312 Dihedral : 7.598 136.194 7465 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 1.12 % Allowed : 11.45 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6529 helix: 1.21 (0.10), residues: 2682 sheet: -0.08 (0.16), residues: 1028 loop : -0.92 (0.12), residues: 2819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 70 HIS 0.005 0.001 HIS 5 188 PHE 0.020 0.001 PHE 6 118 TYR 0.022 0.001 TYR 3 576 ARG 0.003 0.000 ARG F 54 *********************** 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 301 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 235 time to evaluate : 4.623 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: 2 385 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7234 (p90) REVERT: 2 616 ASP cc_start: 0.7769 (m-30) cc_final: 0.7391 (m-30) REVERT: 4 199 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7410 (ptp) REVERT: 4 280 MET cc_start: 0.6631 (mmp) cc_final: 0.6336 (mmm) REVERT: 4 565 LEU cc_start: 0.9230 (tp) cc_final: 0.9011 (tp) REVERT: 4 607 ARG cc_start: 0.7777 (tpt90) cc_final: 0.7431 (tpt90) REVERT: 4 811 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7407 (pmm) REVERT: 5 485 MET cc_start: 0.7629 (ttt) cc_final: 0.7271 (ttp) REVERT: 6 519 MET cc_start: 0.7544 (ptt) cc_final: 0.6963 (ptt) REVERT: 6 629 MET cc_start: 0.8680 (mmm) cc_final: 0.8332 (tpp) REVERT: 6 701 MET cc_start: 0.7459 (ppp) cc_final: 0.7207 (ppp) REVERT: 7 153 MET cc_start: 0.8424 (tmm) cc_final: 0.8129 (tmm) REVERT: 7 343 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8333 (pp) REVERT: 7 402 MET cc_start: 0.7690 (mmm) cc_final: 0.7233 (tpt) REVERT: 7 444 VAL cc_start: 0.3641 (OUTLIER) cc_final: 0.3395 (p) REVERT: 7 638 MET cc_start: 0.8617 (mpp) cc_final: 0.8284 (mpp) REVERT: C 79 MET cc_start: 0.8300 (mmp) cc_final: 0.7999 (mtm) REVERT: D 206 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7902 (pp) REVERT: E 362 MET cc_start: 0.6964 (mmp) cc_final: 0.6693 (mmp) REVERT: F 70 TRP cc_start: 0.6053 (t-100) cc_final: 0.5826 (t-100) REVERT: F 188 MET cc_start: 0.7517 (mpp) cc_final: 0.6976 (tmm) REVERT: G 1798 TRP cc_start: 0.7507 (m-10) cc_final: 0.7231 (m-10) REVERT: I 66 MET cc_start: 0.7336 (mmt) cc_final: 0.7083 (mmt) outliers start: 66 outliers final: 36 residues processed: 289 average time/residue: 0.4720 time to fit residues: 241.2175 Evaluate side-chains 257 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 4.598 ------------------------------------------------------------------------------- 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 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 410 ASP 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 728 TYR Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 533 LEU Chi-restraints excluded: chain 5 residue 553 ILE Chi-restraints excluded: chain 5 residue 752 LEU Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 444 VAL 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 C residue 7 ASP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 315 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 544 ASP Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1877 ASN 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 H residue 182 ASN Chi-restraints excluded: chain I residue 136 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 528 optimal weight: 7.9990 chunk 360 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 472 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 541 optimal weight: 8.9990 chunk 438 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 324 optimal weight: 8.9990 chunk 570 optimal weight: 0.0570 chunk 160 optimal weight: 9.9990 overall best weight: 2.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN ** 2 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 330 HIS ** 7 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 457 GLN ** G1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 53997 Z= 0.245 Angle : 0.572 12.875 73106 Z= 0.292 Chirality : 0.042 0.186 8395 Planarity : 0.004 0.095 9312 Dihedral : 7.682 135.954 7465 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 1.62 % Allowed : 13.14 % Favored : 85.24 % 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: -0.03 (0.11), residues: 6529 helix: 1.08 (0.10), residues: 2692 sheet: -0.25 (0.16), residues: 1016 loop : -0.98 (0.12), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 240 HIS 0.007 0.001 HIS 7 622 PHE 0.019 0.001 PHE 6 118 TYR 0.017 0.001 TYR E 399 ARG 0.003 0.000 ARG 2 205 *********************** 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 325 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 230 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7103 (p90) REVERT: 2 616 ASP cc_start: 0.7744 (m-30) cc_final: 0.7370 (m-30) REVERT: 4 199 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7354 (ptp) REVERT: 4 811 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7380 (pmm) REVERT: 5 485 MET cc_start: 0.7736 (ttt) cc_final: 0.7356 (ttp) REVERT: 5 763 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8582 (mt) REVERT: 6 519 MET cc_start: 0.7604 (ptt) cc_final: 0.7042 (ptt) REVERT: 6 629 MET cc_start: 0.8730 (mmm) cc_final: 0.8379 (tpp) REVERT: 6 701 MET cc_start: 0.7493 (ppp) cc_final: 0.7199 (ppp) REVERT: 7 153 MET cc_start: 0.8452 (tmm) cc_final: 0.8130 (tmm) REVERT: 7 343 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8524 (pp) REVERT: 7 402 MET cc_start: 0.7577 (mmm) cc_final: 0.7190 (tpt) REVERT: 7 444 VAL cc_start: 0.3900 (OUTLIER) cc_final: 0.3658 (p) REVERT: 7 638 MET cc_start: 0.8631 (mpp) cc_final: 0.8288 (mpp) REVERT: C 79 MET cc_start: 0.8304 (mmp) cc_final: 0.7993 (mtm) REVERT: D 129 MET cc_start: 0.8505 (mpp) cc_final: 0.8222 (mpp) REVERT: D 206 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8019 (pp) REVERT: E 380 MET cc_start: 0.8837 (tmm) cc_final: 0.8627 (tmm) REVERT: F 70 TRP cc_start: 0.5741 (t-100) cc_final: 0.5525 (t-100) REVERT: G 1465 MET cc_start: 0.8744 (tmm) cc_final: 0.7788 (mmm) REVERT: G 1798 TRP cc_start: 0.7628 (m-10) cc_final: 0.6998 (m-10) REVERT: I 66 MET cc_start: 0.7327 (mmt) cc_final: 0.7085 (mmt) REVERT: I 172 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8278 (t0) outliers start: 95 outliers final: 58 residues processed: 311 average time/residue: 0.4651 time to fit residues: 256.7580 Evaluate side-chains 284 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 218 time to evaluate : 4.621 ------------------------------------------------------------------------------- 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 559 THR 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 301 LEU Chi-restraints excluded: chain 3 residue 410 ASP 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 728 TYR Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 432 VAL Chi-restraints excluded: chain 5 residue 489 ASP 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 355 ASP 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 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 444 VAL Chi-restraints excluded: chain 7 residue 481 VAL 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 C residue 7 ASP Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 161 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 E residue 607 MET 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 544 ASP Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1877 ASN 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 H residue 182 ASN Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 172 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 213 optimal weight: 7.9990 chunk 571 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 635 optimal weight: 5.9990 chunk 527 optimal weight: 0.0980 chunk 294 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 531 HIS ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 145 GLN ** 7 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN F 55 GLN ** G1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2148 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 53997 Z= 0.213 Angle : 0.546 12.511 73106 Z= 0.279 Chirality : 0.041 0.182 8395 Planarity : 0.004 0.094 9312 Dihedral : 7.605 135.200 7465 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.16 % Rotamer: Outliers : 1.89 % Allowed : 13.82 % Favored : 84.29 % 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: -0.03 (0.10), residues: 6529 helix: 1.11 (0.10), residues: 2679 sheet: -0.24 (0.16), residues: 1016 loop : -0.99 (0.12), residues: 2834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 119 HIS 0.004 0.001 HIS 6 653 PHE 0.018 0.001 PHE F 62 TYR 0.018 0.001 TYR E 399 ARG 0.004 0.000 ARG C 189 *********************** 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 341 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 230 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7252 (p90) REVERT: 2 616 ASP cc_start: 0.7772 (m-30) cc_final: 0.7401 (m-30) REVERT: 2 764 MET cc_start: 0.8353 (mmt) cc_final: 0.8032 (mmt) REVERT: 4 199 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7305 (ptp) REVERT: 4 280 MET cc_start: 0.6452 (mmp) cc_final: 0.6117 (mmm) REVERT: 4 607 ARG cc_start: 0.7814 (tpt90) cc_final: 0.7506 (tpt90) REVERT: 4 801 MET cc_start: 0.8094 (mtp) cc_final: 0.7809 (mpp) REVERT: 4 811 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7415 (pmm) REVERT: 5 172 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8989 (pp) REVERT: 6 519 MET cc_start: 0.7612 (ptt) cc_final: 0.7049 (ptt) REVERT: 6 629 MET cc_start: 0.8718 (mmm) cc_final: 0.8385 (tpp) REVERT: 6 701 MET cc_start: 0.7472 (ppp) cc_final: 0.7125 (ppp) REVERT: 7 153 MET cc_start: 0.8437 (tmm) cc_final: 0.8136 (tmm) REVERT: 7 343 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8450 (pp) REVERT: 7 402 MET cc_start: 0.7494 (mmm) cc_final: 0.7104 (tpt) REVERT: 7 444 VAL cc_start: 0.4120 (OUTLIER) cc_final: 0.3850 (p) REVERT: 7 529 MET cc_start: 0.7463 (ptp) cc_final: 0.6938 (ptp) REVERT: 7 638 MET cc_start: 0.8630 (mpp) cc_final: 0.8294 (mpp) REVERT: C 79 MET cc_start: 0.8270 (mmp) cc_final: 0.7981 (mtm) REVERT: D 129 MET cc_start: 0.8514 (mpp) cc_final: 0.8215 (mpp) REVERT: D 206 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8048 (pp) REVERT: F 188 MET cc_start: 0.7568 (mpp) cc_final: 0.6928 (tmm) REVERT: G 1465 MET cc_start: 0.8764 (tmm) cc_final: 0.7717 (mmm) REVERT: G 1482 MET cc_start: 0.4974 (OUTLIER) cc_final: 0.3934 (mmm) REVERT: G 1798 TRP cc_start: 0.7554 (m-10) cc_final: 0.6699 (m-10) REVERT: I 66 MET cc_start: 0.7323 (mmt) cc_final: 0.7085 (mmt) outliers start: 111 outliers final: 76 residues processed: 323 average time/residue: 0.4547 time to fit residues: 261.5200 Evaluate side-chains 306 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 222 time to evaluate : 4.599 ------------------------------------------------------------------------------- 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 559 THR Chi-restraints excluded: chain 2 residue 567 THR Chi-restraints excluded: chain 2 residue 586 THR Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 100 LEU Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 410 ASP 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 411 THR Chi-restraints excluded: chain 4 residue 505 ASP Chi-restraints excluded: chain 4 residue 646 HIS Chi-restraints excluded: chain 4 residue 728 TYR Chi-restraints excluded: chain 4 residue 811 MET Chi-restraints excluded: chain 5 residue 45 ILE Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 263 GLU Chi-restraints excluded: chain 5 residue 432 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 5 residue 752 LEU Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 355 ASP Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 452 ILE Chi-restraints excluded: chain 6 residue 547 ILE Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 734 LEU Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 444 VAL Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 546 ILE Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 679 PHE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 161 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 E residue 607 MET Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 544 ASP Chi-restraints excluded: chain G residue 1402 LEU Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1482 MET Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1877 ASN 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 104 ASN Chi-restraints excluded: chain H residue 122 ASN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain I residue 6 HIS Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 171 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 657 random chunks: chunk 612 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 362 optimal weight: 0.9990 chunk 464 optimal weight: 0.6980 chunk 359 optimal weight: 6.9990 chunk 535 optimal weight: 20.0000 chunk 354 optimal weight: 9.9990 chunk 633 optimal weight: 5.9990 chunk 396 optimal weight: 0.2980 chunk 386 optimal weight: 8.9990 chunk 292 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 691 ASN 5 636 ASN E 269 ASN F 55 GLN ** F 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1386 ASN ** G1593 GLN ** 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: 0.7777 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 53997 Z= 0.141 Angle : 0.515 12.169 73106 Z= 0.259 Chirality : 0.040 0.177 8395 Planarity : 0.004 0.092 9312 Dihedral : 7.378 132.833 7465 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 1.35 % Allowed : 15.05 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 6529 helix: 1.25 (0.10), residues: 2674 sheet: -0.12 (0.16), residues: 1027 loop : -0.94 (0.12), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP F 70 HIS 0.004 0.001 HIS 3 712 PHE 0.016 0.001 PHE 6 118 TYR 0.016 0.001 TYR E 399 ARG 0.002 0.000 ARG 5 734 *********************** 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 328 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 249 time to evaluate : 4.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 385 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7133 (p90) REVERT: 2 616 ASP cc_start: 0.7770 (m-30) cc_final: 0.7399 (m-30) REVERT: 4 280 MET cc_start: 0.6698 (mmp) cc_final: 0.6032 (mmm) REVERT: 4 356 MET cc_start: 0.6904 (ptp) cc_final: 0.6378 (ptp) REVERT: 4 607 ARG cc_start: 0.7915 (tpt90) cc_final: 0.7534 (tpt90) REVERT: 4 801 MET cc_start: 0.8038 (mtp) cc_final: 0.7792 (mpp) REVERT: 4 811 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7506 (pmm) REVERT: 5 172 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9000 (pp) REVERT: 5 485 MET cc_start: 0.7487 (ttt) cc_final: 0.7164 (ttp) REVERT: 5 689 MET cc_start: 0.6812 (mmm) cc_final: 0.6420 (tpt) REVERT: 5 763 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8619 (mt) REVERT: 6 519 MET cc_start: 0.7557 (ptt) cc_final: 0.7061 (ptt) REVERT: 6 629 MET cc_start: 0.8626 (mmm) cc_final: 0.8315 (tpp) REVERT: 6 701 MET cc_start: 0.7409 (ppp) cc_final: 0.7096 (ppp) REVERT: 7 153 MET cc_start: 0.8395 (tmm) cc_final: 0.8072 (tmm) REVERT: 7 272 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6102 (pm20) REVERT: 7 343 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8347 (pp) REVERT: 7 402 MET cc_start: 0.7536 (mmm) cc_final: 0.7116 (tpt) REVERT: 7 506 MET cc_start: 0.4333 (mmp) cc_final: 0.4094 (mmm) REVERT: 7 529 MET cc_start: 0.7408 (ptp) cc_final: 0.6901 (ptp) REVERT: 7 638 MET cc_start: 0.8618 (mpp) cc_final: 0.8313 (mpp) REVERT: C 79 MET cc_start: 0.8266 (mmp) cc_final: 0.7943 (mtm) REVERT: D 129 MET cc_start: 0.8428 (mpp) cc_final: 0.8108 (mpp) REVERT: D 206 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8022 (pp) REVERT: E 380 MET cc_start: 0.8807 (tmm) cc_final: 0.8581 (tmm) REVERT: F 188 MET cc_start: 0.7503 (mpp) cc_final: 0.6916 (tmm) REVERT: G 1439 MET cc_start: 0.8997 (mtt) cc_final: 0.8590 (mpp) REVERT: G 1465 MET cc_start: 0.8748 (tmm) cc_final: 0.7778 (mmm) REVERT: G 1798 TRP cc_start: 0.7545 (m-10) cc_final: 0.6701 (m-10) REVERT: I 66 MET cc_start: 0.7344 (mmt) cc_final: 0.7108 (mmt) outliers start: 79 outliers final: 60 residues processed: 313 average time/residue: 0.4836 time to fit residues: 266.4761 Evaluate side-chains 296 residues out of total 5944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 229 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 384 ASN 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 619 SER Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 188 LYS Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 301 LEU Chi-restraints excluded: chain 3 residue 410 ASP Chi-restraints excluded: chain 3 residue 733 LEU 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 45 ILE Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 172 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 263 GLU Chi-restraints excluded: chain 5 residue 489 ASP Chi-restraints excluded: chain 5 residue 533 LEU Chi-restraints excluded: chain 5 residue 553 ILE 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 355 ASP 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 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 272 GLU Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 343 LEU Chi-restraints excluded: chain 7 residue 481 VAL 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 64 MET Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 161 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 F residue 544 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 LEU Chi-restraints excluded: chain G residue 1409 GLU Chi-restraints excluded: chain G residue 1532 TYR Chi-restraints excluded: chain G residue 1877 ASN 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 H residue 182 ASN Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 136 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.6253 > 50: distance: 36 - 151: 20.616 distance: 39 - 148: 29.182 distance: 48 - 137: 28.024 distance: 51 - 134: 23.195 distance: 96 - 101: 20.576 distance: 101 - 102: 7.290 distance: 102 - 103: 22.177 distance: 102 - 105: 21.335 distance: 103 - 104: 21.436 distance: 103 - 110: 18.365 distance: 105 - 106: 37.586 distance: 106 - 107: 37.565 distance: 107 - 108: 41.092 distance: 108 - 109: 14.252 distance: 110 - 111: 13.545 distance: 111 - 112: 27.138 distance: 111 - 114: 31.980 distance: 112 - 113: 32.036 distance: 112 - 118: 15.492 distance: 114 - 115: 18.208 distance: 115 - 116: 23.441 distance: 115 - 117: 4.670 distance: 118 - 119: 46.608 distance: 119 - 120: 12.486 distance: 119 - 122: 37.466 distance: 120 - 121: 10.256 distance: 120 - 125: 20.127 distance: 122 - 123: 15.872 distance: 122 - 124: 41.415 distance: 125 - 126: 12.050 distance: 126 - 127: 12.906 distance: 126 - 129: 20.502 distance: 127 - 128: 32.286 distance: 127 - 134: 15.052 distance: 129 - 130: 36.568 distance: 130 - 131: 16.599 distance: 131 - 132: 11.663 distance: 132 - 133: 26.560 distance: 134 - 135: 18.906 distance: 135 - 136: 29.607 distance: 135 - 138: 28.442 distance: 136 - 137: 7.247 distance: 136 - 142: 13.926 distance: 139 - 140: 38.477 distance: 139 - 141: 14.982 distance: 142 - 143: 10.299 distance: 143 - 144: 47.685 distance: 143 - 146: 29.604 distance: 144 - 145: 36.456 distance: 144 - 148: 13.706 distance: 146 - 147: 43.399 distance: 148 - 149: 12.514 distance: 149 - 150: 18.614 distance: 149 - 152: 13.391 distance: 150 - 151: 24.918 distance: 150 - 156: 16.877 distance: 152 - 153: 27.367 distance: 153 - 154: 32.717 distance: 153 - 155: 17.022 distance: 156 - 157: 37.117 distance: 156 - 162: 35.505 distance: 157 - 158: 16.974 distance: 157 - 160: 22.263 distance: 158 - 159: 27.300 distance: 158 - 163: 39.939 distance: 160 - 161: 11.514 distance: 161 - 162: 44.578 distance: 163 - 164: 22.248 distance: 164 - 165: 6.843 distance: 164 - 167: 13.889 distance: 165 - 166: 25.337 distance: 165 - 171: 34.924 distance: 166 - 197: 27.961 distance: 167 - 168: 14.586 distance: 168 - 169: 16.152 distance: 168 - 170: 23.704 distance: 171 - 172: 8.012 distance: 172 - 173: 5.266 distance: 172 - 175: 8.658 distance: 173 - 174: 9.577 distance: 173 - 185: 28.697 distance: 175 - 176: 13.319 distance: 176 - 177: 3.920 distance: 177 - 179: 13.134 distance: 178 - 180: 12.931 distance: 178 - 181: 5.975 distance: 179 - 180: 5.958 distance: 180 - 182: 11.537 distance: 181 - 183: 13.335 distance: 182 - 184: 9.697 distance: 183 - 184: 14.283