Starting phenix.real_space_refine on Mon Mar 11 09:23:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/03_2024/7odt_12847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/03_2024/7odt_12847.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/03_2024/7odt_12847_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/03_2024/7odt_12847_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/03_2024/7odt_12847_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/03_2024/7odt_12847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/03_2024/7odt_12847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/03_2024/7odt_12847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/03_2024/7odt_12847_updated.pdb" } resolution = 3.1 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= 0.006 sd= 0.105 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: 9 Type Number sf(0) Gaussians K 10 8.98 5 Fe 2 7.16 5 Zn 2 6.06 5 P 1528 5.49 5 Mg 95 5.21 5 S 338 5.16 5 C 64170 2.51 5 N 20005 2.21 5 O 24323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 110473 Number of models: 1 Model: "" Number of chains: 71 Chain: "t" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2398 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 14, 'TRANS': 301} Chain breaks: 2 Chain: "u" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 919 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "x" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2750 Classifications: {'peptide': 346} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Chain: "y" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1980 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "0" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 898 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "1" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "3" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 832 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 342 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3210 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 361} Chain: "6" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2948 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 319} Chain: "7" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2390 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 276} Chain: "8" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 91} Chain: "9" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 113} Chain: "A" Number of atoms: 30850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1453, 30850 Classifications: {'RNA': 1453} Modifications used: {'rna2p_pur': 159, 'rna2p_pyr': 109, 'rna3p': 2, 'rna3p_pur': 607, 'rna3p_pyr': 576} Link IDs: {'rna2p': 267, 'rna3p': 1185} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1522 Classifications: {'RNA': 72} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 8, 'rna3p': 63} Chain: "D" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1872 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 13, 'TRANS': 226} Chain: "E" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2406 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 280} Chain: "F" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2031 Classifications: {'peptide': 252} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 230} Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "I" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1358 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 15, 'TRANS': 152} Chain: "J" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1330 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 165} Chain: "K" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1455 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 161} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 890 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2327 Classifications: {'peptide': 291} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 264} Chain: "N" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1786 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain: "O" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1259 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "P" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1173 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 136} Chain: "Q" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1843 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206} Chain: "R" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1154 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1293 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 149} Chain: "T" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1369 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "U" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1251 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 139} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1676 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 186} Chain: "W" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 835 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "X" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2044 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain: "Y" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1556 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "Z" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 996 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 11, 'TRANS': 110} Chain: "a" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 840 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 88} Chain breaks: 1 Chain: "b" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1189 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 9, 'TRANS': 139} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'THC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2299 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 268} Chain breaks: 1 Chain: "d" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2124 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 20, 'TRANS': 238} Chain: "e" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1848 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Chain: "f" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1196 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain breaks: 1 Chain: "g" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1113 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 117} Chain: "h" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 895 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "i" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 828 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 745 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Chain: "k" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 774 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 688 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 8, 'TRANS': 73} Chain: "m" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 419 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "o" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 798 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "p" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 2 Chain: "q" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1177 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 14, 'TRANS': 126} Chain: "r" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1322 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 142} Chain: "s" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3155 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 358} Chain breaks: 1 Chain: "t" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PM8': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Unusual residues: {' K': 10, ' MG': 88} Classifications: {'undetermined': 98} Link IDs: {None: 97} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9537 SG CYS 0 110 133.694 106.144 212.861 1.00 84.36 S ATOM 9559 SG CYS 0 113 137.371 107.342 212.782 1.00 77.68 S ATOM 9639 SG CYS 0 123 135.979 105.483 209.831 1.00 69.32 S ATOM 9662 SG CYS 0 126 136.387 103.684 213.207 1.00 76.49 S ATOM 11929 SG CYS 4 76 64.104 104.979 122.887 1.00 88.18 S ATOM 11952 SG CYS 4 79 66.819 106.733 124.887 1.00 87.17 S ATOM 12076 SG CYS 4 92 64.741 103.965 126.491 1.00 81.99 S ATOM 62352 SG CYS I 64 65.148 145.705 127.582 1.00 98.75 S ATOM A04P8 SG CYS r 73 62.033 146.383 129.694 1.00 87.11 S ATOM A04ON SG CYS r 70 61.028 142.502 131.025 1.00 78.99 S ATOM A04XE SG CYS r 108 63.484 140.238 129.406 1.00 73.16 S Time building chain proxies: 41.24, per 1000 atoms: 0.37 Number of scatterers: 110473 At special positions: 0 Unit cell: (257.58, 223.66, 254.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 Fe 2 26.01 K 10 19.00 S 338 16.00 P 1528 15.00 Mg 95 11.99 O 24323 8.00 N 20005 7.00 C 64170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 36.01 Conformation dependent library (CDL) restraints added in 10.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES r 201 " pdb="FE2 FES r 201 " - pdb=" SG CYS r 70 " pdb="FE1 FES r 201 " - pdb=" SG CYS I 64 " pdb="FE1 FES r 201 " - pdb=" SG CYS r 73 " pdb="FE2 FES r 201 " - pdb=" SG CYS r 108 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN 0 201 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 123 " pdb=" ZN 4 201 " pdb="ZN ZN 4 201 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 92 " Number of angles added : 9 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18034 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 329 helices and 81 sheets defined 43.0% alpha, 13.5% beta 333 base pairs and 839 stacking pairs defined. Time for finding SS restraints: 58.96 Creating SS restraints... Processing helix chain 't' and resid 191 through 197 removed outlier: 4.138A pdb=" N PHE t 195 " --> pdb=" O GLY t 191 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU t 196 " --> pdb=" O ASN t 192 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA t 197 " --> pdb=" O ARG t 193 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 191 through 197' Processing helix chain 't' and resid 236 through 246 Processing helix chain 't' and resid 293 through 302 removed outlier: 3.971A pdb=" N ARG t 302 " --> pdb=" O ARG t 298 " (cutoff:3.500A) Processing helix chain 't' and resid 316 through 332 Processing helix chain 't' and resid 333 through 339 removed outlier: 3.586A pdb=" N ALA t 337 " --> pdb=" O LYS t 333 " (cutoff:3.500A) Proline residue: t 339 - end of helix Processing helix chain 't' and resid 346 through 351 Proline residue: t 350 - end of helix No H-bonds generated for 'chain 't' and resid 346 through 351' Processing helix chain 't' and resid 352 through 363 Processing helix chain 't' and resid 377 through 400 removed outlier: 3.728A pdb=" N LEU t 381 " --> pdb=" O ASN t 377 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS t 384 " --> pdb=" O GLN t 380 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA t 391 " --> pdb=" O VAL t 387 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR t 392 " --> pdb=" O LEU t 388 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 105 Processing helix chain 'u' and resid 131 through 149 removed outlier: 3.651A pdb=" N VAL u 143 " --> pdb=" O ALA u 139 " (cutoff:3.500A) Processing helix chain 'u' and resid 181 through 189 removed outlier: 3.697A pdb=" N ILE u 187 " --> pdb=" O GLU u 183 " (cutoff:3.500A) Processing helix chain 'u' and resid 190 through 197 Processing helix chain 'v' and resid 5 through 24 removed outlier: 3.604A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ARG v 24 " --> pdb=" O GLY v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 45 removed outlier: 3.586A pdb=" N PHE v 39 " --> pdb=" O ILE v 35 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS v 41 " --> pdb=" O ARG v 37 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN v 43 " --> pdb=" O PHE v 39 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS v 44 " --> pdb=" O ARG v 40 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU v 45 " --> pdb=" O LYS v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 47 through 64 removed outlier: 3.691A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL v 60 " --> pdb=" O GLU v 56 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.679A pdb=" N ILE w 79 " --> pdb=" O THR w 75 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN w 80 " --> pdb=" O LEU w 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 5.139A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.389A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU w 138 " --> pdb=" O ASP w 134 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N MET w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 removed outlier: 3.523A pdb=" N ASP w 150 " --> pdb=" O ASP w 146 " (cutoff:3.500A) Processing helix chain 'w' and resid 103 through 109 removed outlier: 3.524A pdb=" N LEU w 108 " --> pdb=" O HIS w 103 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 57 removed outlier: 4.052A pdb=" N VAL x 54 " --> pdb=" O MET x 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 58 through 70 removed outlier: 4.515A pdb=" N SER x 62 " --> pdb=" O ASP x 58 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER x 66 " --> pdb=" O SER x 62 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU x 70 " --> pdb=" O SER x 66 " (cutoff:3.500A) Processing helix chain 'x' and resid 82 through 94 removed outlier: 3.646A pdb=" N LEU x 93 " --> pdb=" O LYS x 89 " (cutoff:3.500A) Processing helix chain 'x' and resid 97 through 109 removed outlier: 3.521A pdb=" N TRP x 106 " --> pdb=" O ALA x 102 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU x 107 " --> pdb=" O ILE x 103 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU x 108 " --> pdb=" O SER x 104 " (cutoff:3.500A) Processing helix chain 'x' and resid 159 through 170 removed outlier: 3.752A pdb=" N LEU x 163 " --> pdb=" O ASP x 159 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU x 164 " --> pdb=" O ALA x 160 " (cutoff:3.500A) Proline residue: x 165 - end of helix removed outlier: 3.959A pdb=" N GLY x 170 " --> pdb=" O VAL x 166 " (cutoff:3.500A) Processing helix chain 'x' and resid 185 through 195 removed outlier: 4.259A pdb=" N ALA x 190 " --> pdb=" O GLY x 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU x 192 " --> pdb=" O THR x 188 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY x 195 " --> pdb=" O LEU x 191 " (cutoff:3.500A) Processing helix chain 'x' and resid 206 through 221 Processing helix chain 'x' and resid 222 through 228 removed outlier: 3.810A pdb=" N ARG x 226 " --> pdb=" O PRO x 222 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY x 228 " --> pdb=" O GLU x 224 " (cutoff:3.500A) Processing helix chain 'x' and resid 237 through 244 removed outlier: 4.148A pdb=" N TRP x 241 " --> pdb=" O ASP x 237 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY x 242 " --> pdb=" O GLY x 238 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU x 243 " --> pdb=" O ARG x 239 " (cutoff:3.500A) Processing helix chain 'x' and resid 260 through 267 removed outlier: 3.852A pdb=" N HIS x 266 " --> pdb=" O ARG x 262 " (cutoff:3.500A) Processing helix chain 'x' and resid 274 through 300 removed outlier: 4.808A pdb=" N LYS x 279 " --> pdb=" O ARG x 275 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU x 280 " --> pdb=" O SER x 276 " (cutoff:3.500A) Proline residue: x 285 - end of helix removed outlier: 5.727A pdb=" N LYS x 300 " --> pdb=" O LEU x 296 " (cutoff:3.500A) Processing helix chain 'x' and resid 313 through 331 removed outlier: 4.715A pdb=" N TYR x 319 " --> pdb=" O LEU x 315 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL x 320 " --> pdb=" O GLN x 316 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL x 321 " --> pdb=" O ASN x 317 " (cutoff:3.500A) Processing helix chain 'x' and resid 341 through 350 removed outlier: 3.732A pdb=" N VAL x 347 " --> pdb=" O HIS x 343 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE x 348 " --> pdb=" O PHE x 344 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP x 350 " --> pdb=" O ARG x 346 " (cutoff:3.500A) Processing helix chain 'y' and resid 88 through 103 removed outlier: 3.577A pdb=" N VAL y 95 " --> pdb=" O GLU y 91 " (cutoff:3.500A) Processing helix chain 'y' and resid 105 through 116 Processing helix chain 'y' and resid 120 through 135 Processing helix chain 'y' and resid 137 through 149 Proline residue: y 149 - end of helix Processing helix chain 'y' and resid 155 through 170 removed outlier: 3.502A pdb=" N MET y 159 " --> pdb=" O PRO y 155 " (cutoff:3.500A) Processing helix chain 'y' and resid 173 through 183 removed outlier: 6.212A pdb=" N LYS y 177 " --> pdb=" O GLU y 173 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG y 178 " --> pdb=" O GLY y 174 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL y 179 " --> pdb=" O LYS y 175 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR y 181 " --> pdb=" O LYS y 177 " (cutoff:3.500A) Processing helix chain 'y' and resid 190 through 203 removed outlier: 3.615A pdb=" N ILE y 194 " --> pdb=" O ARG y 190 " (cutoff:3.500A) Processing helix chain 'y' and resid 208 through 219 Processing helix chain 'y' and resid 220 through 226 removed outlier: 4.502A pdb=" N ARG y 224 " --> pdb=" O PRO y 220 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP y 226 " --> pdb=" O VAL y 222 " (cutoff:3.500A) Processing helix chain 'y' and resid 227 through 239 removed outlier: 3.638A pdb=" N ALA y 237 " --> pdb=" O LYS y 233 " (cutoff:3.500A) Processing helix chain 'y' and resid 244 through 252 Processing helix chain 'y' and resid 257 through 272 Processing helix chain 'y' and resid 289 through 295 Processing helix chain 'y' and resid 297 through 305 Processing helix chain 'y' and resid 309 through 331 removed outlier: 3.700A pdb=" N PHE y 313 " --> pdb=" O SER y 309 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 95 removed outlier: 3.504A pdb=" N CYS 0 92 " --> pdb=" O GLU 0 88 " (cutoff:3.500A) Processing helix chain '0' and resid 96 through 101 removed outlier: 5.336A pdb=" N ILE 0 101 " --> pdb=" O PRO 0 97 " (cutoff:3.500A) Processing helix chain '0' and resid 123 through 146 Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 72 removed outlier: 4.120A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 73 through 86 removed outlier: 3.576A pdb=" N VAL 2 78 " --> pdb=" O ALA 2 74 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 114 removed outlier: 3.662A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 4.040A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 137' Processing helix chain '3' and resid 138 through 147 removed outlier: 3.524A pdb=" N ARG 3 143 " --> pdb=" O ALA 3 139 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE 3 147 " --> pdb=" O ARG 3 143 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 3.601A pdb=" N LYS 3 160 " --> pdb=" O LYS 3 156 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET 3 161 " --> pdb=" O LEU 3 157 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR 3 162 " --> pdb=" O LEU 3 158 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 5.362A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 4.512A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) Proline residue: 5 53 - end of helix No H-bonds generated for 'chain '5' and resid 47 through 53' Processing helix chain '5' and resid 116 through 125 removed outlier: 3.570A pdb=" N TRP 5 122 " --> pdb=" O LYS 5 118 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 142 removed outlier: 3.663A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP 5 142 " --> pdb=" O SER 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 163 Processing helix chain '5' and resid 172 through 196 removed outlier: 3.508A pdb=" N TYR 5 176 " --> pdb=" O LYS 5 172 " (cutoff:3.500A) Proline residue: 5 178 - end of helix removed outlier: 3.649A pdb=" N VAL 5 181 " --> pdb=" O CYS 5 177 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU 5 184 " --> pdb=" O ILE 5 180 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS 5 194 " --> pdb=" O SER 5 190 " (cutoff:3.500A) Proline residue: 5 196 - end of helix Processing helix chain '5' and resid 241 through 252 removed outlier: 3.820A pdb=" N THR 5 248 " --> pdb=" O GLU 5 244 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.261A pdb=" N LEU 5 304 " --> pdb=" O ARG 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 407 through 420 removed outlier: 4.315A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 3.773A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA 6 67 " --> pdb=" O GLN 6 63 " (cutoff:3.500A) Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 78 removed outlier: 3.824A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 116 removed outlier: 3.557A pdb=" N ASN 6 116 " --> pdb=" O GLU 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 117 through 126 Processing helix chain '6' and resid 131 through 143 removed outlier: 3.608A pdb=" N ARG 6 141 " --> pdb=" O ALA 6 137 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 156 removed outlier: 3.521A pdb=" N TYR 6 155 " --> pdb=" O LEU 6 151 " (cutoff:3.500A) Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 244 through 249 removed outlier: 3.889A pdb=" N GLY 6 248 " --> pdb=" O ARG 6 244 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN 6 249 " --> pdb=" O VAL 6 245 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 244 through 249' Processing helix chain '6' and resid 292 through 297 Processing helix chain '6' and resid 299 through 308 removed outlier: 3.581A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 removed outlier: 4.138A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE 6 330 " --> pdb=" O SER 6 326 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 371 removed outlier: 3.581A pdb=" N ARG 6 368 " --> pdb=" O ARG 6 364 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 removed outlier: 3.946A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 removed outlier: 4.013A pdb=" N THR 7 41 " --> pdb=" O PRO 7 37 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU 7 42 " --> pdb=" O THR 7 38 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET 7 43 " --> pdb=" O GLU 7 39 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG 7 44 " --> pdb=" O LEU 7 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) Proline residue: 7 60 - end of helix Processing helix chain '7' and resid 87 through 96 removed outlier: 3.526A pdb=" N HIS 7 94 " --> pdb=" O SER 7 90 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU 7 95 " --> pdb=" O CYS 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 103 Processing helix chain '7' and resid 135 through 158 removed outlier: 3.608A pdb=" N VAL 7 153 " --> pdb=" O MET 7 149 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE 7 154 " --> pdb=" O MET 7 150 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 7 155 " --> pdb=" O GLY 7 151 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG 7 156 " --> pdb=" O CYS 7 152 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 191 removed outlier: 4.053A pdb=" N ASP 7 190 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU 7 191 " --> pdb=" O SER 7 187 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 186 through 191' Processing helix chain '7' and resid 195 through 213 removed outlier: 3.526A pdb=" N PHE 7 202 " --> pdb=" O ASN 7 198 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 222 through 231 removed outlier: 3.616A pdb=" N ILE 7 229 " --> pdb=" O VAL 7 225 " (cutoff:3.500A) Processing helix chain '7' and resid 233 through 248 removed outlier: 3.662A pdb=" N VAL 7 237 " --> pdb=" O SER 7 233 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP 7 238 " --> pdb=" O LYS 7 234 " (cutoff:3.500A) Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 323 removed outlier: 3.577A pdb=" N LYS 7 315 " --> pdb=" O THR 7 311 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG 7 319 " --> pdb=" O LYS 7 315 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N MET 7 323 " --> pdb=" O ARG 7 319 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 3.688A pdb=" N CYS 7 275 " --> pdb=" O THR 7 272 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 107 through 154 removed outlier: 3.548A pdb=" N LYS 8 119 " --> pdb=" O ALA 8 115 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS 8 120 " --> pdb=" O LEU 8 116 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU 8 123 " --> pdb=" O LYS 8 119 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU 8 128 " --> pdb=" O TYR 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 155 through 163 removed outlier: 3.728A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) Processing helix chain '9' and resid 27 through 35 removed outlier: 5.713A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.522A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 96 Processing helix chain '9' and resid 97 through 107 Processing helix chain '9' and resid 113 through 118 Processing helix chain 'D' and resid 259 through 267 removed outlier: 4.078A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 Processing helix chain 'D' and resid 289 through 296 removed outlier: 4.480A pdb=" N SER D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.645A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.705A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.556A pdb=" N GLU E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 168 " --> pdb=" O PHE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.896A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARG E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 199' Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 108 removed outlier: 4.567A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.545A pdb=" N ARG F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 removed outlier: 3.753A pdb=" N LEU F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.716A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 4.399A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 4.926A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.044A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.732A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 85 through 90 removed outlier: 4.190A pdb=" N ARG H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Proline residue: H 90 - end of helix No H-bonds generated for 'chain 'H' and resid 85 through 90' Processing helix chain 'H' and resid 115 through 122 removed outlier: 3.658A pdb=" N ARG H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 149 removed outlier: 3.554A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.745A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 66 Proline residue: I 66 - end of helix Processing helix chain 'I' and resid 76 through 92 removed outlier: 3.599A pdb=" N ARG I 84 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.639A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 138 Proline residue: I 133 - end of helix removed outlier: 3.866A pdb=" N ASP I 137 " --> pdb=" O PRO I 133 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.950A pdb=" N PHE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 143 through 148' Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.685A pdb=" N ARG I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'J' and resid 33 through 43 Proline residue: J 37 - end of helix removed outlier: 3.670A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 58 Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.535A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 4.109A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 134 Processing helix chain 'J' and resid 136 through 152 removed outlier: 3.533A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 151 " --> pdb=" O SER J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 192 removed outlier: 4.291A pdb=" N ALA J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 40 removed outlier: 3.599A pdb=" N ILE K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG K 38 " --> pdb=" O MET K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 101 through 112 removed outlier: 3.634A pdb=" N MET K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.587A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.693A pdb=" N ASN K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 167 Proline residue: K 167 - end of helix Processing helix chain 'K' and resid 70 through 75 removed outlier: 4.262A pdb=" N LYS K 75 " --> pdb=" O ASN K 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 70 through 75' Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.508A pdb=" N ARG L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 126 through 131' Processing helix chain 'L' and resid 133 through 142 removed outlier: 4.871A pdb=" N VAL L 137 " --> pdb=" O GLU L 133 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 20 removed outlier: 3.585A pdb=" N ALA M 10 " --> pdb=" O GLN M 6 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU M 13 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU M 15 " --> pdb=" O ARG M 11 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU M 16 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG M 17 " --> pdb=" O LEU M 13 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.600A pdb=" N ARG M 59 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 79 removed outlier: 3.533A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Proline residue: M 79 - end of helix Processing helix chain 'M' and resid 86 through 91 removed outlier: 6.056A pdb=" N ARG M 91 " --> pdb=" O HIS M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 108 Processing helix chain 'M' and resid 117 through 125 Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.663A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY M 171 " --> pdb=" O ILE M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 removed outlier: 3.526A pdb=" N ASP M 185 " --> pdb=" O PRO M 181 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE M 186 " --> pdb=" O ARG M 182 " (cutoff:3.500A) Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 removed outlier: 3.853A pdb=" N ARG M 196 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY M 197 " --> pdb=" O PHE M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 216 Proline residue: M 212 - end of helix removed outlier: 3.556A pdb=" N ASP M 216 " --> pdb=" O PRO M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 241 removed outlier: 3.785A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix removed outlier: 3.510A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 251 removed outlier: 4.057A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU M 251 " --> pdb=" O ILE M 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 246 through 251' Processing helix chain 'M' and resid 252 through 258 Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.525A pdb=" N SER M 296 " --> pdb=" O LYS M 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 74 removed outlier: 4.126A pdb=" N ARG N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLY N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 69 through 74' Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 168 through 184 removed outlier: 3.744A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN N 178 " --> pdb=" O GLY N 174 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS N 182 " --> pdb=" O GLN N 178 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU N 183 " --> pdb=" O VAL N 179 " (cutoff:3.500A) Proline residue: N 184 - end of helix Processing helix chain 'N' and resid 191 through 209 Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 225 through 231 removed outlier: 4.776A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.434A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 66 removed outlier: 4.037A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.313A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.735A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix Processing helix chain 'O' and resid 143 through 162 Processing helix chain 'P' and resid 52 through 60 removed outlier: 4.576A pdb=" N LEU P 56 " --> pdb=" O ASN P 52 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU P 57 " --> pdb=" O PRO P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 117 removed outlier: 4.809A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR P 117 " --> pdb=" O LYS P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 140 Processing helix chain 'P' and resid 149 through 156 removed outlier: 5.575A pdb=" N ASP P 156 " --> pdb=" O GLU P 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 169 Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.255A pdb=" N ILE Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Proline residue: Q 82 - end of helix No H-bonds generated for 'chain 'Q' and resid 77 through 82' Processing helix chain 'Q' and resid 88 through 106 removed outlier: 3.867A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 193 removed outlier: 4.676A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 4.294A pdb=" N SER Q 198 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 4.045A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.720A pdb=" N GLN Q 258 " --> pdb=" O MET Q 254 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.036A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 292 removed outlier: 3.559A pdb=" N ALA Q 280 " --> pdb=" O SER Q 276 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA Q 281 " --> pdb=" O LYS Q 277 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.599A pdb=" N GLU R 23 " --> pdb=" O PHE R 19 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 44 removed outlier: 4.134A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 64 removed outlier: 3.773A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 80 removed outlier: 3.517A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.712A pdb=" N ASN R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 109 through 134 removed outlier: 4.869A pdb=" N ASP R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 90 removed outlier: 3.817A pdb=" N ARG S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE S 87 " --> pdb=" O VAL S 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL S 88 " --> pdb=" O ASN S 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY S 90 " --> pdb=" O MET S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.591A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 150 through 155' Processing helix chain 'T' and resid 43 through 51 removed outlier: 3.907A pdb=" N LYS T 47 " --> pdb=" O ARG T 43 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN T 49 " --> pdb=" O TRP T 45 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS T 50 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE T 51 " --> pdb=" O LYS T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 89 removed outlier: 4.080A pdb=" N TYR T 83 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU T 84 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE T 88 " --> pdb=" O LEU T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 103 removed outlier: 3.813A pdb=" N PHE T 102 " --> pdb=" O ALA T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 125 removed outlier: 4.121A pdb=" N LYS T 109 " --> pdb=" O LYS T 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 200 removed outlier: 3.663A pdb=" N ARG T 200 " --> pdb=" O GLN T 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 112 through 118 Proline residue: U 118 - end of helix Processing helix chain 'U' and resid 124 through 138 removed outlier: 5.063A pdb=" N GLN U 138 " --> pdb=" O ARG U 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 36 Proline residue: V 36 - end of helix Processing helix chain 'V' and resid 50 through 55 removed outlier: 5.757A pdb=" N TYR V 55 " --> pdb=" O ASP V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 121 removed outlier: 5.043A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 184 removed outlier: 3.730A pdb=" N GLU V 184 " --> pdb=" O GLU V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 121 removed outlier: 3.501A pdb=" N LEU W 116 " --> pdb=" O GLU W 112 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU W 120 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Proline residue: W 121 - end of helix Processing helix chain 'X' and resid 7 through 19 removed outlier: 3.663A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU X 16 " --> pdb=" O LYS X 12 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 35 removed outlier: 5.893A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 4.117A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 79' Processing helix chain 'X' and resid 128 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 192 removed outlier: 3.569A pdb=" N TYR X 191 " --> pdb=" O ILE X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 204 removed outlier: 4.768A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL X 204 " --> pdb=" O GLU X 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 245 removed outlier: 3.541A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.888A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 63 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 5.833A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 4.021A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.948A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.378A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.869A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 3.828A pdb=" N LYS Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 193 through 198' Processing helix chain 'Y' and resid 202 through 239 removed outlier: 4.302A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS Y 236 " --> pdb=" O LYS Y 232 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS Y 237 " --> pdb=" O ILE Y 233 " (cutoff:3.500A) Proline residue: Y 239 - end of helix Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.217A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA Z 48 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 48' Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.640A pdb=" N GLU Z 54 " --> pdb=" O PRO Z 50 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS Z 55 " --> pdb=" O GLU Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 114 removed outlier: 3.677A pdb=" N VAL Z 112 " --> pdb=" O ALA Z 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 135 removed outlier: 3.520A pdb=" N MET Z 134 " --> pdb=" O ALA Z 130 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 130 through 135' Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 119 through 124 removed outlier: 4.486A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR a 124 " --> pdb=" O LYS a 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 119 through 124' Processing helix chain 'a' and resid 127 through 134 Processing helix chain 'b' and resid 2 through 7 Proline residue: b 7 - end of helix Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.735A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 37 through 50 removed outlier: 3.988A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 59 Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 108 removed outlier: 5.660A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 137 removed outlier: 4.668A pdb=" N ASN b 135 " --> pdb=" O HIS b 131 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS b 136 " --> pdb=" O PRO b 132 " (cutoff:3.500A) Proline residue: b 137 - end of helix No H-bonds generated for 'chain 'b' and resid 131 through 137' Processing helix chain 'c' and resid 34 through 54 removed outlier: 5.302A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Proline residue: c 54 - end of helix Processing helix chain 'c' and resid 59 through 64 removed outlier: 3.528A pdb=" N LYS c 63 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Proline residue: c 64 - end of helix No H-bonds generated for 'chain 'c' and resid 59 through 64' Processing helix chain 'c' and resid 67 through 80 removed outlier: 3.515A pdb=" N PHE c 75 " --> pdb=" O GLU c 71 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY c 76 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS c 77 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.626A pdb=" N THR c 90 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE c 92 " --> pdb=" O LEU c 88 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 109 removed outlier: 3.665A pdb=" N ARG c 105 " --> pdb=" O GLU c 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c 108 " --> pdb=" O LYS c 104 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 146 Proline residue: c 146 - end of helix Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 removed outlier: 3.724A pdb=" N CYS c 167 " --> pdb=" O GLU c 163 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN c 172 " --> pdb=" O HIS c 168 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU c 173 " --> pdb=" O VAL c 169 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA c 174 " --> pdb=" O ALA c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 224 removed outlier: 3.734A pdb=" N LEU c 213 " --> pdb=" O GLU c 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE c 214 " --> pdb=" O ARG c 210 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.552A pdb=" N MET c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 removed outlier: 3.667A pdb=" N GLU c 243 " --> pdb=" O GLY c 239 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG c 248 " --> pdb=" O GLU c 244 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 49 through 54 removed outlier: 3.805A pdb=" N LYS d 54 " --> pdb=" O PHE d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.790A pdb=" N SER d 99 " --> pdb=" O ALA d 95 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 115 Processing helix chain 'd' and resid 116 through 130 removed outlier: 3.726A pdb=" N ILE d 122 " --> pdb=" O SER d 118 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG d 123 " --> pdb=" O GLN d 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG d 124 " --> pdb=" O VAL d 120 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 134 through 155 Proline residue: d 138 - end of helix removed outlier: 3.540A pdb=" N LYS d 142 " --> pdb=" O PRO d 138 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP d 143 " --> pdb=" O GLU d 139 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU d 152 " --> pdb=" O ALA d 148 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.661A pdb=" N HIS d 161 " --> pdb=" O HIS d 157 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU d 163 " --> pdb=" O ARG d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 177 Proline residue: d 170 - end of helix removed outlier: 4.575A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE d 176 " --> pdb=" O MET d 172 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 85 through 101 Processing helix chain 'e' and resid 116 through 132 removed outlier: 3.514A pdb=" N MET e 123 " --> pdb=" O ASP e 119 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP e 124 " --> pdb=" O LEU e 120 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 144 Processing helix chain 'e' and resid 183 through 195 removed outlier: 3.555A pdb=" N ALA e 188 " --> pdb=" O LEU e 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU e 192 " --> pdb=" O ALA e 188 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 218 through 223 removed outlier: 6.323A pdb=" N ARG e 222 " --> pdb=" O PRO e 218 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR e 223 " --> pdb=" O GLN e 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 218 through 223' Processing helix chain 'e' and resid 256 through 264 removed outlier: 4.634A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR e 263 " --> pdb=" O GLU e 259 " (cutoff:3.500A) Processing helix chain 'e' and resid 265 through 277 removed outlier: 3.824A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.815A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 59 through 64' Processing helix chain 'f' and resid 99 through 118 Processing helix chain 'f' and resid 164 through 178 removed outlier: 4.167A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE f 169 " --> pdb=" O THR f 165 " (cutoff:3.500A) Processing helix chain 'f' and resid 200 through 212 removed outlier: 3.510A pdb=" N GLU f 206 " --> pdb=" O PRO f 202 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU f 207 " --> pdb=" O GLU f 203 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU f 211 " --> pdb=" O LEU f 207 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 53 removed outlier: 5.488A pdb=" N TYR g 45 " --> pdb=" O SER g 41 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLN g 46 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE g 47 " --> pdb=" O ASP g 43 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG g 50 " --> pdb=" O GLN g 46 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU g 52 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Proline residue: g 53 - end of helix Processing helix chain 'g' and resid 116 through 132 removed outlier: 3.892A pdb=" N LEU g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 removed outlier: 3.613A pdb=" N LYS g 164 " --> pdb=" O TRP g 160 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 79 Processing helix chain 'h' and resid 93 through 108 Processing helix chain 'h' and resid 113 through 121 removed outlier: 4.760A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.611A pdb=" N VAL h 126 " --> pdb=" O ARG h 122 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 147 removed outlier: 5.437A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 54 Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 74 removed outlier: 3.858A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 74' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 Processing helix chain 'j' and resid 24 through 32 Processing helix chain 'j' and resid 36 through 41 removed outlier: 4.600A pdb=" N TYR j 40 " --> pdb=" O ASN j 36 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLY j 41 " --> pdb=" O PRO j 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 36 through 41' Processing helix chain 'j' and resid 60 through 108 removed outlier: 3.724A pdb=" N GLN j 102 " --> pdb=" O LEU j 98 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG j 103 " --> pdb=" O GLN j 99 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN j 105 " --> pdb=" O GLU j 101 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU j 106 " --> pdb=" O GLN j 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN j 107 " --> pdb=" O ARG j 103 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA j 108 " --> pdb=" O LYS j 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 9 removed outlier: 3.933A pdb=" N LEU k 8 " --> pdb=" O ALA k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 39 removed outlier: 3.642A pdb=" N SER k 39 " --> pdb=" O GLN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 47 removed outlier: 3.600A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN k 46 " --> pdb=" O VAL k 42 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU k 47 " --> pdb=" O ARG k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 102 Processing helix chain 'l' and resid 64 through 71 Processing helix chain 'l' and resid 72 through 77 removed outlier: 4.237A pdb=" N ASN l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE l 77 " --> pdb=" O MET l 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 72 through 77' Processing helix chain 'l' and resid 88 through 93 removed outlier: 3.801A pdb=" N TYR l 92 " --> pdb=" O PRO l 88 " (cutoff:3.500A) Proline residue: l 93 - end of helix No H-bonds generated for 'chain 'l' and resid 88 through 93' Processing helix chain 'l' and resid 94 through 99 removed outlier: 4.275A pdb=" N GLU l 98 " --> pdb=" O GLU l 94 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET l 99 " --> pdb=" O TRP l 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 94 through 99' Processing helix chain 'l' and resid 106 through 111 removed outlier: 3.598A pdb=" N LEU l 110 " --> pdb=" O THR l 106 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP l 111 " --> pdb=" O LEU l 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 106 through 111' Processing helix chain 'l' and resid 114 through 136 removed outlier: 3.679A pdb=" N TRP l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN l 135 " --> pdb=" O ARG l 131 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS l 136 " --> pdb=" O LEU l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 39 removed outlier: 5.156A pdb=" N ALA m 38 " --> pdb=" O ASP m 34 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER m 39 " --> pdb=" O SER m 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 34 through 39' Processing helix chain 'o' and resid 28 through 52 removed outlier: 3.680A pdb=" N TYR o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Proline residue: o 52 - end of helix Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 63 through 81 removed outlier: 3.998A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 3.907A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LYS o 100 " --> pdb=" O ASN o 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 50 Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 73 through 78 removed outlier: 4.075A pdb=" N LEU p 77 " --> pdb=" O PRO p 73 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 73 through 78' Processing helix chain 'p' and resid 112 through 123 removed outlier: 3.540A pdb=" N ILE p 121 " --> pdb=" O GLN p 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 164 Processing helix chain 'p' and resid 173 through 190 removed outlier: 4.234A pdb=" N ARG p 177 " --> pdb=" O VAL p 173 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE p 180 " --> pdb=" O HIS p 176 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG p 187 " --> pdb=" O MET p 183 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG p 189 " --> pdb=" O ARG p 185 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.610A pdb=" N THR p 57 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA p 58 " --> pdb=" O SER p 55 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TRP p 59 " --> pdb=" O ASP p 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'q' and resid 48 through 53 removed outlier: 4.132A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 54 through 65 Processing helix chain 'q' and resid 71 through 76 removed outlier: 4.588A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP q 76 " --> pdb=" O PRO q 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 71 through 76' Processing helix chain 'q' and resid 78 through 93 removed outlier: 3.632A pdb=" N ARG q 83 " --> pdb=" O PRO q 79 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU q 84 " --> pdb=" O GLU q 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 165 removed outlier: 3.553A pdb=" N LYS q 127 " --> pdb=" O GLU q 123 " (cutoff:3.500A) Proline residue: q 129 - end of helix Processing helix chain 'r' and resid 70 through 76 removed outlier: 3.730A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.009A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 removed outlier: 3.503A pdb=" N ARG r 113 " --> pdb=" O GLN r 109 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 183 removed outlier: 4.288A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP r 183 " --> pdb=" O PRO r 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 178 through 183' Processing helix chain 's' and resid 55 through 74 removed outlier: 3.592A pdb=" N HIS s 71 " --> pdb=" O GLN s 67 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLU s 74 " --> pdb=" O VAL s 70 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.554A pdb=" N TYR s 108 " --> pdb=" O ARG s 104 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 155 removed outlier: 3.549A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS s 154 " --> pdb=" O LEU s 150 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 193 removed outlier: 4.851A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU s 170 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER s 173 " --> pdb=" O SER s 169 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU s 174 " --> pdb=" O GLU s 170 " (cutoff:3.500A) Proline residue: s 175 - end of helix Proline residue: s 190 - end of helix Proline residue: s 193 - end of helix Processing helix chain 's' and resid 194 through 199 removed outlier: 3.909A pdb=" N ALA s 198 " --> pdb=" O ALA s 194 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALA s 199 " --> pdb=" O LEU s 195 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 194 through 199' Processing helix chain 's' and resid 267 through 272 removed outlier: 4.781A pdb=" N LEU s 271 " --> pdb=" O LYS s 267 " (cutoff:3.500A) Proline residue: s 272 - end of helix No H-bonds generated for 'chain 's' and resid 267 through 272' Processing helix chain 's' and resid 307 through 315 removed outlier: 3.564A pdb=" N LEU s 312 " --> pdb=" O ARG s 308 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG s 313 " --> pdb=" O GLU s 309 " (cutoff:3.500A) Processing helix chain 's' and resid 317 through 344 removed outlier: 5.000A pdb=" N GLU s 321 " --> pdb=" O ALA s 317 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY s 344 " --> pdb=" O ALA s 340 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 388 removed outlier: 3.667A pdb=" N GLN s 385 " --> pdb=" O THR s 381 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Proline residue: s 388 - end of helix Processing helix chain 's' and resid 414 through 427 removed outlier: 3.907A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 't' and resid 170 through 173 removed outlier: 4.697A pdb=" N THR t 161 " --> pdb=" O LEU t 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS t 164 " --> pdb=" O HIS t 218 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY t 209 " --> pdb=" O GLY t 86 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY t 86 " --> pdb=" O GLY t 209 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASN t 84 " --> pdb=" O PRO t 211 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN t 213 " --> pdb=" O GLY t 82 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N GLN t 133 " --> pdb=" O VAL t 114 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL t 114 " --> pdb=" O GLN t 133 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE t 135 " --> pdb=" O GLY t 112 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY t 137 " --> pdb=" O ASN t 110 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASN t 110 " --> pdb=" O GLY t 137 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP t 139 " --> pdb=" O GLY t 108 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLY t 108 " --> pdb=" O ASP t 139 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY t 141 " --> pdb=" O GLY t 106 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL t 114 " --> pdb=" O ALA t 182 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP t 178 " --> pdb=" O VAL t 118 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 't' and resid 227 through 231 removed outlier: 3.567A pdb=" N ALA t 341 " --> pdb=" O LEU t 306 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 't' and resid 261 through 268 Processing sheet with id= 4, first strand: chain 't' and resid 82 through 86 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 't' and resid 107 through 114 removed outlier: 4.350A pdb=" N GLY t 189 " --> pdb=" O GLY t 108 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASN t 110 " --> pdb=" O ALA t 187 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA t 187 " --> pdb=" O ASN t 110 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY t 112 " --> pdb=" O GLY t 185 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY t 185 " --> pdb=" O GLY t 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA t 183 " --> pdb=" O VAL t 114 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'u' and resid 107 through 114 removed outlier: 3.645A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY u 129 " --> pdb=" O MET u 180 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'x' and resid 130 through 133 removed outlier: 4.974A pdb=" N ARG x 130 " --> pdb=" O VAL x 77 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'x' and resid 230 through 236 removed outlier: 3.922A pdb=" N TRP x 236 " --> pdb=" O ASP x 204 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG x 251 " --> pdb=" O ILE x 176 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP x 255 " --> pdb=" O LEU x 180 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP x 250 " --> pdb=" O GLY x 302 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY x 303 " --> pdb=" O ARG x 382 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER x 311 " --> pdb=" O PRO x 374 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS x 379 " --> pdb=" O GLU x 339 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'x' and resid 361 through 365 Processing sheet with id= 10, first strand: chain '0' and resid 155 through 161 Processing sheet with id= 11, first strand: chain '1' and resid 16 through 22 removed outlier: 6.073A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '1' and resid 41 through 46 removed outlier: 6.310A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '4' and resid 66 through 70 removed outlier: 5.473A pdb=" N HIS 4 98 " --> pdb=" O CYS 4 92 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N CYS 4 92 " --> pdb=" O HIS 4 98 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '5' and resid 126 through 130 removed outlier: 5.348A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '5' and resid 208 through 214 removed outlier: 4.375A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '6' and resid 183 through 187 removed outlier: 3.592A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '6' and resid 231 through 234 removed outlier: 3.510A pdb=" N TYR 6 232 " --> pdb=" O SER 6 220 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '6' and resid 311 through 314 removed outlier: 6.715A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '6' and resid 213 through 220 removed outlier: 3.980A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '7' and resid 77 through 82 removed outlier: 4.446A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS 7 123 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS 7 68 " --> pdb=" O CYS 7 123 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '7' and resid 164 through 167 removed outlier: 3.740A pdb=" N PHE 7 297 " --> pdb=" O TYR 7 181 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '7' and resid 217 through 221 Processing sheet with id= 23, first strand: chain '9' and resid 42 through 45 removed outlier: 3.604A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.580A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP D 180 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 190 through 193 removed outlier: 3.645A pdb=" N VAL D 215 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 138 through 144 removed outlier: 5.112A pdb=" N ASP D 138 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG D 147 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'E' and resid 98 through 101 removed outlier: 3.517A pdb=" N VAL E 206 " --> pdb=" O GLU E 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 208 " --> pdb=" O ARG E 266 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.854A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 176 through 182 removed outlier: 6.715A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 275 through 278 removed outlier: 8.072A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 32, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 33, first strand: chain 'H' and resid 55 through 58 removed outlier: 7.142A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'H' and resid 94 through 97 Processing sheet with id= 35, first strand: chain 'I' and resid 121 through 125 removed outlier: 5.615A pdb=" N HIS I 150 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET I 95 " --> pdb=" O SER I 156 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.901A pdb=" N GLY J 18 " --> pdb=" O VAL J 72 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'K' and resid 55 through 60 removed outlier: 3.522A pdb=" N GLU K 143 " --> pdb=" O TRP K 18 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'L' and resid 58 through 61 removed outlier: 3.770A pdb=" N HIS L 59 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN L 72 " --> pdb=" O TYR L 61 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 40, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 41, first strand: chain 'N' and resid 94 through 97 Processing sheet with id= 42, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.663A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.357A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.483A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 130 through 135 removed outlier: 6.363A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 139 through 143 removed outlier: 3.988A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG Q 143 " --> pdb=" O GLY Q 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY Q 146 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 105 through 109 removed outlier: 7.019A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE S 141 " --> pdb=" O ALA S 138 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 111 through 117 removed outlier: 3.922A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.811A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.039A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'T' and resid 65 through 72 removed outlier: 4.743A pdb=" N ALA T 65 " --> pdb=" O GLU T 174 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS T 171 " --> pdb=" O ALA T 137 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN T 133 " --> pdb=" O GLY T 175 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 138 through 144 removed outlier: 3.749A pdb=" N GLU T 138 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR T 165 " --> pdb=" O GLY T 144 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 146 through 153 removed outlier: 3.719A pdb=" N LEU T 147 " --> pdb=" O LYS T 163 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG T 157 " --> pdb=" O HIS T 153 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'U' and resid 38 through 44 removed outlier: 6.934A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA U 67 " --> pdb=" O GLN U 98 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 60 through 65 removed outlier: 4.308A pdb=" N ASP V 60 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS V 72 " --> pdb=" O ILE V 64 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'V' and resid 78 through 81 removed outlier: 3.771A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'V' and resid 92 through 97 removed outlier: 6.074A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 75 through 78 removed outlier: 6.339A pdb=" N VAL W 133 " --> pdb=" O GLY W 78 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'W' and resid 80 through 84 removed outlier: 7.547A pdb=" N HIS W 80 " --> pdb=" O LEU W 92 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'X' and resid 49 through 53 removed outlier: 5.230A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'X' and resid 85 through 91 Processing sheet with id= 62, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 63, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.144A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'a' and resid 45 through 52 removed outlier: 6.199A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'b' and resid 61 through 68 removed outlier: 3.852A pdb=" N ARG b 74 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL b 75 " --> pdb=" O GLU b 86 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU b 86 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA b 77 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL b 84 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR b 79 " --> pdb=" O GLY b 82 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 67, first strand: chain 'c' and resid 269 through 275 removed outlier: 3.842A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'd' and resid 212 through 219 removed outlier: 6.732A pdb=" N TYR d 245 " --> pdb=" O LYS d 264 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS d 264 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'e' and resid 174 through 178 removed outlier: 5.997A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'e' and resid 197 through 201 removed outlier: 7.691A pdb=" N GLU e 197 " --> pdb=" O SER e 244 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN e 199 " --> pdb=" O ASP e 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR e 240 " --> pdb=" O GLU e 201 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'e' and resid 211 through 216 removed outlier: 3.753A pdb=" N GLY e 211 " --> pdb=" O PHE e 233 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE e 215 " --> pdb=" O ALA e 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA e 229 " --> pdb=" O PHE e 215 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'e' and resid 44 through 53 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'f' and resid 90 through 98 removed outlier: 5.485A pdb=" N GLU f 154 " --> pdb=" O PRO f 128 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL f 156 " --> pdb=" O ALA f 126 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA f 126 " --> pdb=" O VAL f 156 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL f 134 " --> pdb=" O ASP f 147 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.578A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'k' and resid 49 through 56 removed outlier: 3.834A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG k 56 " --> pdb=" O PHE k 20 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'm' and resid 62 through 66 removed outlier: 4.770A pdb=" N SER m 62 " --> pdb=" O LYS m 58 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'p' and resid 79 through 83 Processing sheet with id= 78, first strand: chain 'r' and resid 35 through 42 removed outlier: 3.729A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 's' and resid 90 through 93 removed outlier: 4.062A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 's' and resid 112 through 116 Processing sheet with id= 81, first strand: chain 's' and resid 297 through 302 removed outlier: 5.566A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) 2864 hydrogen bonds defined for protein. 8508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 790 hydrogen bonds 1362 hydrogen bond angles 0 basepair planarities 333 basepair parallelities 839 stacking parallelities Total time for adding SS restraints: 71.19 Time building geometry restraints manager: 39.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 46266 1.41 - 1.61: 68133 1.61 - 1.80: 1555 1.80 - 2.00: 103 2.00 - 2.20: 4 Bond restraints: 116061 Sorted by residual: bond pdb=" C1' SAM x 401 " pdb=" C2' SAM x 401 " ideal model delta sigma weight residual 1.307 1.518 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C1' SAM x 401 " pdb=" O4' SAM x 401 " ideal model delta sigma weight residual 1.616 1.412 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C2 OMU A3039 " pdb=" N3 OMU A3039 " ideal model delta sigma weight residual 1.499 1.323 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N3 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 1.492 1.344 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" N3 OMU A3039 " pdb=" C4 OMU A3039 " ideal model delta sigma weight residual 1.457 1.325 0.132 2.00e-02 2.50e+03 4.37e+01 ... (remaining 116056 not shown) Histogram of bond angle deviations from ideal: 75.00 - 87.21: 2 87.21 - 99.43: 1 99.43 - 111.65: 64674 111.65 - 123.87: 91136 123.87 - 136.08: 8439 Bond angle restraints: 164252 Sorted by residual: angle pdb=" C4' OMU A3039 " pdb=" C3' OMU A3039 " pdb=" C2' OMU A3039 " ideal model delta sigma weight residual 102.60 96.07 6.53 1.00e+00 1.00e+00 4.26e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 108.29 125.63 -17.34 3.00e+00 1.11e-01 3.34e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C8 OMG A3040 " ideal model delta sigma weight residual 142.82 125.54 17.28 3.00e+00 1.11e-01 3.32e+01 angle pdb=" P OMG A3040 " pdb=" O5' OMG A3040 " pdb=" C5' OMG A3040 " ideal model delta sigma weight residual 120.90 112.31 8.59 1.50e+00 4.44e-01 3.28e+01 angle pdb=" C ASP s 407 " pdb=" CA ASP s 407 " pdb=" CB ASP s 407 " ideal model delta sigma weight residual 116.54 110.42 6.12 1.15e+00 7.56e-01 2.84e+01 ... (remaining 164247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 68273 35.85 - 71.71: 2903 71.71 - 107.56: 462 107.56 - 143.42: 7 143.42 - 179.27: 23 Dihedral angle restraints: 71668 sinusoidal: 43783 harmonic: 27885 Sorted by residual: dihedral pdb=" O4' U A2898 " pdb=" C1' U A2898 " pdb=" N1 U A2898 " pdb=" C2 U A2898 " ideal model delta sinusoidal sigma weight residual -160.00 18.73 -178.73 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2493 " pdb=" C1' C A2493 " pdb=" N1 C A2493 " pdb=" C2 C A2493 " ideal model delta sinusoidal sigma weight residual 200.00 30.27 169.73 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' C A2379 " pdb=" C1' C A2379 " pdb=" N1 C A2379 " pdb=" C2 C A2379 " ideal model delta sinusoidal sigma weight residual 200.00 38.18 161.82 1 1.50e+01 4.44e-03 8.32e+01 ... (remaining 71665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 16282 0.039 - 0.078: 1979 0.078 - 0.117: 831 0.117 - 0.156: 54 0.156 - 0.195: 7 Chirality restraints: 19153 Sorted by residual: chirality pdb=" C2' U A3038 " pdb=" C3' U A3038 " pdb=" O2' U A3038 " pdb=" C1' U A3038 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" C3' C A2186 " pdb=" C4' C A2186 " pdb=" O3' C A2186 " pdb=" C2' C A2186 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" C2' U A3037 " pdb=" C3' U A3037 " pdb=" O2' U A3037 " pdb=" C1' U A3037 " both_signs ideal model delta sigma weight residual False -2.75 -2.58 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 19150 not shown) Planarity restraints: 15513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A3040 " 0.091 2.00e-02 2.50e+03 5.77e-01 7.49e+03 pdb=" C4' OMG A3040 " 0.449 2.00e-02 2.50e+03 pdb=" O4' OMG A3040 " 0.512 2.00e-02 2.50e+03 pdb=" C3' OMG A3040 " -0.624 2.00e-02 2.50e+03 pdb=" O3' OMG A3040 " -0.650 2.00e-02 2.50e+03 pdb=" C2' OMG A3040 " -0.176 2.00e-02 2.50e+03 pdb=" O2' OMG A3040 " 0.977 2.00e-02 2.50e+03 pdb=" C1' OMG A3040 " 0.237 2.00e-02 2.50e+03 pdb=" N9 OMG A3040 " -0.817 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SAM x 401 " -0.349 2.00e-02 2.50e+03 3.45e-01 2.68e+03 pdb=" C2' SAM x 401 " 0.444 2.00e-02 2.50e+03 pdb=" C3' SAM x 401 " 0.448 2.00e-02 2.50e+03 pdb=" C4' SAM x 401 " -0.340 2.00e-02 2.50e+03 pdb=" C5' SAM x 401 " 0.300 2.00e-02 2.50e+03 pdb=" N9 SAM x 401 " 0.313 2.00e-02 2.50e+03 pdb=" O2' SAM x 401 " -0.205 2.00e-02 2.50e+03 pdb=" O3' SAM x 401 " -0.204 2.00e-02 2.50e+03 pdb=" O4' SAM x 401 " -0.407 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 PM8 w 200 " -0.022 2.00e-02 2.50e+03 7.73e-02 7.47e+01 pdb=" C34 PM8 w 200 " -0.022 2.00e-02 2.50e+03 pdb=" C37 PM8 w 200 " 0.091 2.00e-02 2.50e+03 pdb=" N36 PM8 w 200 " -0.122 2.00e-02 2.50e+03 pdb=" O35 PM8 w 200 " 0.076 2.00e-02 2.50e+03 ... (remaining 15510 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.62: 1434 2.62 - 3.25: 104071 3.25 - 3.88: 232841 3.88 - 4.51: 323946 4.51 - 5.14: 465912 Nonbonded interactions: 1128204 Sorted by model distance: nonbonded pdb=" OP1 C A2915 " pdb="MG MG A3344 " model vdw 1.988 2.170 nonbonded pdb=" OP1 A A1961 " pdb="MG MG A3314 " model vdw 1.992 2.170 nonbonded pdb=" OP1 U A2035 " pdb="MG MG A3344 " model vdw 1.994 2.170 nonbonded pdb=" OP1 A A2509 " pdb="MG MG A3332 " model vdw 2.012 2.170 nonbonded pdb=" O4 U A2475 " pdb="MG MG A3331 " model vdw 2.016 2.170 ... (remaining 1128199 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 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: 0.100 Extract box with map and model: 21.100 Check model and map are aligned: 1.180 Set scattering table: 0.750 Process input model: 318.510 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 351.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.211 116061 Z= 0.159 Angle : 0.415 17.336 164252 Z= 0.230 Chirality : 0.031 0.195 19153 Planarity : 0.006 0.577 15513 Dihedral : 16.424 179.273 53634 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.53 % Allowed : 1.55 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 9449 helix: 1.10 (0.09), residues: 3161 sheet: 0.32 (0.14), residues: 1336 loop : 0.73 (0.09), residues: 4952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP s 346 HIS 0.002 0.000 HIS D 100 PHE 0.009 0.001 PHE x 38 TYR 0.012 0.001 TYR 5 176 ARG 0.003 0.000 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1838 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1793 time to evaluate : 7.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 164 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7810 (ptmm) REVERT: t 224 VAL cc_start: 0.5109 (OUTLIER) cc_final: 0.4654 (m) REVERT: t 265 ILE cc_start: 0.5229 (OUTLIER) cc_final: 0.4896 (tp) REVERT: t 357 SER cc_start: 0.8325 (t) cc_final: 0.8104 (m) REVERT: t 365 GLN cc_start: 0.3693 (OUTLIER) cc_final: 0.3162 (pt0) REVERT: u 101 LEU cc_start: 0.8215 (mt) cc_final: 0.7570 (mt) REVERT: u 167 TRP cc_start: 0.7522 (t60) cc_final: 0.7240 (t60) REVERT: u 169 CYS cc_start: 0.6134 (m) cc_final: 0.5690 (m) REVERT: u 171 ASP cc_start: 0.7614 (t0) cc_final: 0.6601 (t0) REVERT: u 180 MET cc_start: 0.7541 (ptt) cc_final: 0.7286 (pmm) REVERT: u 191 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: u 192 LYS cc_start: 0.7451 (tttt) cc_final: 0.7023 (ttmm) REVERT: v 22 GLN cc_start: 0.6449 (mm110) cc_final: 0.5836 (mt0) REVERT: v 40 ARG cc_start: 0.6436 (mtm180) cc_final: 0.5495 (tpt170) REVERT: v 53 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7641 (mmm-85) REVERT: x 58 ASP cc_start: 0.6373 (t70) cc_final: 0.5917 (t0) REVERT: x 83 TRP cc_start: 0.6464 (p-90) cc_final: 0.6082 (p-90) REVERT: x 208 SER cc_start: 0.8483 (t) cc_final: 0.8205 (p) REVERT: y 96 MET cc_start: 0.5224 (ptp) cc_final: 0.4846 (ppp) REVERT: y 187 PHE cc_start: 0.6035 (m-80) cc_final: 0.5630 (m-80) REVERT: y 291 LYS cc_start: 0.6369 (pttp) cc_final: 0.5471 (mtmm) REVERT: 0 155 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6270 (mp0) REVERT: 0 160 TYR cc_start: 0.6151 (m-80) cc_final: 0.5696 (m-80) REVERT: 6 119 GLU cc_start: 0.7755 (mm-30) cc_final: 0.6988 (tp30) REVERT: 6 243 ASN cc_start: 0.5452 (OUTLIER) cc_final: 0.5038 (t0) REVERT: 7 165 ASN cc_start: 0.8129 (m-40) cc_final: 0.7680 (p0) REVERT: 7 207 HIS cc_start: 0.8310 (m90) cc_final: 0.7998 (m-70) REVERT: 7 284 HIS cc_start: 0.4817 (m-70) cc_final: 0.4525 (m170) REVERT: 8 171 PHE cc_start: 0.7009 (t80) cc_final: 0.6783 (t80) REVERT: 9 76 TYR cc_start: 0.7690 (m-80) cc_final: 0.7171 (m-80) REVERT: E 77 LEU cc_start: 0.7560 (mt) cc_final: 0.7297 (tt) REVERT: E 139 ASN cc_start: 0.6552 (t0) cc_final: 0.6002 (m-40) REVERT: F 101 MET cc_start: 0.7935 (mmp) cc_final: 0.7686 (mmp) REVERT: F 231 VAL cc_start: 0.8676 (t) cc_final: 0.8336 (p) REVERT: H 134 PRO cc_start: 0.8006 (Cg_exo) cc_final: 0.7795 (Cg_endo) REVERT: I 115 GLN cc_start: 0.4835 (mt0) cc_final: 0.4621 (tt0) REVERT: I 166 ARG cc_start: 0.5129 (ptt-90) cc_final: 0.4056 (ptm-80) REVERT: J 30 MET cc_start: 0.3065 (mmm) cc_final: 0.2835 (mmp) REVERT: J 79 GLU cc_start: 0.4763 (tt0) cc_final: 0.3772 (pm20) REVERT: J 115 LYS cc_start: 0.6963 (mttt) cc_final: 0.6702 (mptt) REVERT: J 134 ASP cc_start: 0.6550 (m-30) cc_final: 0.6343 (m-30) REVERT: J 170 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6882 (pp20) REVERT: L 95 ARG cc_start: 0.6831 (mpp-170) cc_final: 0.6381 (mmp80) REVERT: M 261 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7199 (t0) REVERT: N 242 TRP cc_start: 0.8156 (t-100) cc_final: 0.7930 (t-100) REVERT: O 75 MET cc_start: 0.8079 (mmt) cc_final: 0.7852 (mmm) REVERT: Q 99 MET cc_start: 0.8817 (mtm) cc_final: 0.8483 (mtm) REVERT: T 127 ASN cc_start: 0.7991 (t0) cc_final: 0.7774 (t0) REVERT: T 133 ASN cc_start: 0.8305 (t0) cc_final: 0.7883 (t0) REVERT: V 52 GLU cc_start: 0.5826 (mt-10) cc_final: 0.5277 (tm-30) REVERT: W 93 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7617 (mm-30) REVERT: Z 52 ASP cc_start: 0.7688 (m-30) cc_final: 0.7479 (m-30) REVERT: Z 80 TYR cc_start: 0.8674 (p90) cc_final: 0.8434 (p90) REVERT: a 102 HIS cc_start: 0.6196 (t70) cc_final: 0.5617 (p90) REVERT: c 90 THR cc_start: 0.8155 (p) cc_final: 0.7798 (t) REVERT: c 97 TYR cc_start: 0.8327 (t80) cc_final: 0.8103 (t80) REVERT: d 248 PHE cc_start: 0.6422 (m-80) cc_final: 0.6183 (m-80) REVERT: e 66 LEU cc_start: 0.3635 (tp) cc_final: 0.2888 (mm) REVERT: e 143 LYS cc_start: 0.7855 (tttt) cc_final: 0.7509 (pttt) REVERT: e 224 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7240 (tm-30) REVERT: f 60 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7640 (ttmt) REVERT: f 96 THR cc_start: 0.5391 (m) cc_final: 0.5120 (p) REVERT: f 113 LEU cc_start: 0.6751 (tp) cc_final: 0.6405 (tp) REVERT: h 67 GLN cc_start: 0.6774 (tt0) cc_final: 0.6541 (tt0) REVERT: h 68 SER cc_start: 0.8522 (m) cc_final: 0.8176 (p) REVERT: h 96 LEU cc_start: 0.8433 (mt) cc_final: 0.8103 (pp) REVERT: h 97 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7467 (mtpt) REVERT: h 122 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6680 (mmt90) REVERT: h 157 SER cc_start: 0.7569 (m) cc_final: 0.7012 (p) REVERT: k 7 ARG cc_start: 0.6893 (mtt180) cc_final: 0.6622 (mmt180) REVERT: k 11 ARG cc_start: 0.5777 (mmm160) cc_final: 0.5391 (tpp80) REVERT: k 27 VAL cc_start: 0.8347 (m) cc_final: 0.7977 (t) REVERT: k 46 ASN cc_start: 0.6820 (t0) cc_final: 0.6479 (m110) REVERT: k 76 MET cc_start: 0.6316 (mtm) cc_final: 0.5605 (mtp) REVERT: l 58 ASP cc_start: 0.1368 (OUTLIER) cc_final: 0.0955 (p0) REVERT: l 113 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6241 (pm20) REVERT: l 127 TRP cc_start: 0.6370 (m-10) cc_final: 0.6069 (m100) REVERT: l 134 LYS cc_start: 0.5831 (tttp) cc_final: 0.5440 (tptt) REVERT: m 58 LYS cc_start: 0.6419 (mttt) cc_final: 0.5971 (mmtm) REVERT: p 182 ASN cc_start: 0.8774 (m-40) cc_final: 0.8360 (m110) REVERT: q 82 LEU cc_start: 0.8473 (tp) cc_final: 0.8121 (tt) REVERT: q 85 LEU cc_start: 0.8434 (tp) cc_final: 0.8223 (mp) REVERT: q 144 GLU cc_start: 0.7885 (tt0) cc_final: 0.7481 (tm-30) REVERT: q 155 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7447 (ttp-170) REVERT: r 190 THR cc_start: 0.8071 (m) cc_final: 0.7727 (p) outliers start: 45 outliers final: 11 residues processed: 1829 average time/residue: 1.1681 time to fit residues: 3587.3112 Evaluate side-chains 911 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 893 time to evaluate : 6.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 128 VAL Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 224 VAL Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain u residue 191 GLU Chi-restraints excluded: chain x residue 29 LYS Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 6 residue 243 ASN Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 261 ASP Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain l residue 58 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 918 optimal weight: 6.9990 chunk 824 optimal weight: 6.9990 chunk 457 optimal weight: 10.0000 chunk 281 optimal weight: 8.9990 chunk 556 optimal weight: 5.9990 chunk 440 optimal weight: 8.9990 chunk 852 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 518 optimal weight: 9.9990 chunk 634 optimal weight: 0.9990 chunk 988 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 120 GLN t 121 GLN t 199 ASN t 234 ASN t 271 HIS t 273 GLN t 362 HIS u 136 HIS v 19 GLN v 63 ASN x 109 GLN x 172 GLN x 230 GLN x 316 GLN ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 122 GLN y 123 GLN y 235 GLN y 255 GLN y 284 GLN 1 31 ASN 1 52 GLN 5 165 GLN 5 266 HIS ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN 7 290 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN E 117 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 GLN K 40 GLN K 74 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 GLN N 68 ASN N 237 HIS ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 HIS P 162 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 HIS S 118 ASN T 73 GLN T 126 HIS ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 101 HIS V 78 GLN Y 179 HIS Z 64 HIS a 46 ASN b 107 GLN ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 GLN d 58 GLN d 167 HIS d 262 HIS e 67 GLN e 75 GLN f 158 GLN g 65 HIS g 92 HIS h 131 ASN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN k 35 GLN l 82 GLN m 65 HIS o 94 HIS p 117 GLN q 161 GLN r 79 HIS r 96 HIS r 112 HIS s 239 ASN s 343 GLN s 358 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 116061 Z= 0.339 Angle : 0.638 20.799 164252 Z= 0.320 Chirality : 0.041 0.301 19153 Planarity : 0.005 0.125 15513 Dihedral : 19.529 179.289 33525 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.27 % Allowed : 7.59 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.95 (0.08), residues: 9449 helix: 1.15 (0.09), residues: 3259 sheet: 0.19 (0.14), residues: 1316 loop : 0.57 (0.09), residues: 4874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP x 106 HIS 0.024 0.002 HIS I 114 PHE 0.021 0.002 PHE N 175 TYR 0.027 0.002 TYR h 73 ARG 0.013 0.001 ARG m 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 927 time to evaluate : 7.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 132 TYR cc_start: 0.5176 (m-80) cc_final: 0.4793 (m-80) REVERT: t 229 MET cc_start: 0.2583 (ttm) cc_final: 0.1866 (ttt) REVERT: t 365 GLN cc_start: 0.3793 (OUTLIER) cc_final: 0.3130 (pt0) REVERT: u 97 MET cc_start: 0.7981 (tmm) cc_final: 0.7761 (tmm) REVERT: u 118 MET cc_start: 0.6084 (mmm) cc_final: 0.5642 (mmm) REVERT: u 180 MET cc_start: 0.7361 (ptt) cc_final: 0.7140 (ptp) REVERT: x 58 ASP cc_start: 0.6372 (t70) cc_final: 0.5924 (t0) REVERT: x 83 TRP cc_start: 0.6307 (p-90) cc_final: 0.5758 (p-90) REVERT: x 369 MET cc_start: 0.6521 (mmm) cc_final: 0.6264 (mmm) REVERT: y 169 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5891 (mt) REVERT: y 267 TYR cc_start: 0.7864 (t80) cc_final: 0.7504 (t80) REVERT: y 291 LYS cc_start: 0.6191 (pttp) cc_final: 0.5565 (mtmm) REVERT: y 316 PHE cc_start: 0.6950 (t80) cc_final: 0.6711 (t80) REVERT: 0 170 GLN cc_start: 0.7343 (mt0) cc_final: 0.7055 (mm110) REVERT: 1 32 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8164 (p) REVERT: 6 119 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7063 (tp30) REVERT: 7 115 MET cc_start: 0.8320 (mmm) cc_final: 0.7815 (mmm) REVERT: E 77 LEU cc_start: 0.7598 (mt) cc_final: 0.7331 (tt) REVERT: I 166 ARG cc_start: 0.5734 (ptt-90) cc_final: 0.4490 (ptm-80) REVERT: J 79 GLU cc_start: 0.5223 (tt0) cc_final: 0.3966 (pm20) REVERT: J 170 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7101 (pp20) REVERT: P 55 ASN cc_start: 0.8167 (t0) cc_final: 0.7957 (t0) REVERT: Q 99 MET cc_start: 0.8586 (mtm) cc_final: 0.8354 (mtm) REVERT: S 87 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7778 (mm) REVERT: U 48 MET cc_start: 0.7836 (ttt) cc_final: 0.7521 (ttt) REVERT: V 66 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: V 78 GLN cc_start: 0.5132 (OUTLIER) cc_final: 0.4222 (tm130) REVERT: X 233 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: a 102 HIS cc_start: 0.6288 (t70) cc_final: 0.5623 (p-80) REVERT: b 50 GLU cc_start: 0.7388 (tp30) cc_final: 0.7005 (tt0) REVERT: d 57 MET cc_start: 0.4879 (tmm) cc_final: 0.3993 (pmm) REVERT: d 248 PHE cc_start: 0.6461 (m-80) cc_final: 0.6044 (m-80) REVERT: d 256 TYR cc_start: 0.6762 (m-80) cc_final: 0.6447 (m-80) REVERT: d 261 MET cc_start: 0.6846 (ttp) cc_final: 0.6577 (ttp) REVERT: e 66 LEU cc_start: 0.3864 (tp) cc_final: 0.3294 (mm) REVERT: e 143 LYS cc_start: 0.7892 (tttt) cc_final: 0.7519 (pttt) REVERT: e 221 MET cc_start: 0.0623 (mtm) cc_final: 0.0375 (mtm) REVERT: e 224 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7287 (tm-30) REVERT: h 122 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6733 (mmt90) REVERT: j 103 ARG cc_start: 0.7685 (ptm-80) cc_final: 0.7359 (mtp-110) REVERT: k 11 ARG cc_start: 0.5844 (mmm160) cc_final: 0.5477 (tpp80) REVERT: k 27 VAL cc_start: 0.7832 (m) cc_final: 0.7568 (t) REVERT: k 76 MET cc_start: 0.6491 (mtm) cc_final: 0.5887 (mtp) REVERT: k 92 SER cc_start: 0.6391 (p) cc_final: 0.6038 (m) REVERT: l 58 ASP cc_start: 0.1362 (OUTLIER) cc_final: 0.0934 (p0) REVERT: l 99 MET cc_start: 0.0993 (mmt) cc_final: 0.0773 (mmt) REVERT: l 113 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6346 (pm20) REVERT: l 123 LYS cc_start: 0.6640 (tttt) cc_final: 0.5427 (tttp) REVERT: l 127 TRP cc_start: 0.6023 (m-10) cc_final: 0.5798 (m100) REVERT: l 134 LYS cc_start: 0.5869 (tttp) cc_final: 0.5568 (tptt) REVERT: m 51 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.5198 (tp) REVERT: m 58 LYS cc_start: 0.6942 (mttt) cc_final: 0.6377 (mmtm) REVERT: p 182 ASN cc_start: 0.8681 (m-40) cc_final: 0.8292 (m-40) REVERT: q 82 LEU cc_start: 0.8646 (tp) cc_final: 0.8168 (tt) REVERT: q 144 GLU cc_start: 0.7915 (tt0) cc_final: 0.7469 (tm-30) REVERT: q 155 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7646 (ptt-90) REVERT: q 156 LEU cc_start: 0.7630 (mt) cc_final: 0.7329 (tp) REVERT: r 76 ASN cc_start: 0.7744 (m110) cc_final: 0.7311 (m110) REVERT: r 190 THR cc_start: 0.8084 (m) cc_final: 0.7712 (p) outliers start: 191 outliers final: 116 residues processed: 1057 average time/residue: 0.9613 time to fit residues: 1759.1941 Evaluate side-chains 910 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 785 time to evaluate : 7.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 204 VAL Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 195 THR Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 169 LEU Chi-restraints excluded: chain y residue 223 LEU Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 179 VAL Chi-restraints excluded: chain 6 residue 187 VAL Chi-restraints excluded: chain 6 residue 280 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 9 residue 127 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 156 ASP Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 233 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 116 GLU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain b residue 40 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 89 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 84 SER Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain l residue 58 ASP Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain p residue 78 THR Chi-restraints excluded: chain p residue 132 GLU Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 50 GLU Chi-restraints excluded: chain r residue 116 GLU Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 148 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 549 optimal weight: 7.9990 chunk 306 optimal weight: 8.9990 chunk 822 optimal weight: 8.9990 chunk 672 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 989 optimal weight: 4.9990 chunk 1069 optimal weight: 0.7980 chunk 881 optimal weight: 7.9990 chunk 981 optimal weight: 30.0000 chunk 337 optimal weight: 20.0000 chunk 794 optimal weight: 6.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 198 ASN t 314 GLN t 380 GLN ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 185 ASN 5 165 GLN ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 320 GLN 7 84 ASN 7 165 ASN 7 207 HIS ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS F 223 HIS ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN I 128 ASN I 129 GLN I 151 ASN K 40 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 GLN V 78 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 220 GLN e 67 GLN g 93 ASN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 HIS p 117 GLN p 194 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 116061 Z= 0.383 Angle : 0.650 17.755 164252 Z= 0.328 Chirality : 0.042 0.249 19153 Planarity : 0.005 0.129 15513 Dihedral : 19.678 179.550 33510 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.87 % Allowed : 8.84 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.54 (0.08), residues: 9449 helix: 0.88 (0.09), residues: 3282 sheet: -0.06 (0.14), residues: 1319 loop : 0.27 (0.09), residues: 4848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 229 HIS 0.018 0.001 HIS I 114 PHE 0.023 0.002 PHE x 372 TYR 0.024 0.002 TYR t 268 ARG 0.008 0.001 ARG r 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 826 time to evaluate : 7.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 229 MET cc_start: 0.2709 (ttm) cc_final: 0.1973 (ttt) REVERT: t 361 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6003 (m-30) REVERT: t 365 GLN cc_start: 0.4010 (OUTLIER) cc_final: 0.3207 (pt0) REVERT: t 379 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5579 (tm-30) REVERT: u 118 MET cc_start: 0.5731 (mmm) cc_final: 0.5313 (mmm) REVERT: u 180 MET cc_start: 0.7427 (ptt) cc_final: 0.7168 (ptp) REVERT: v 40 ARG cc_start: 0.6895 (mtm180) cc_final: 0.6026 (tpm170) REVERT: w 111 ASP cc_start: 0.6770 (OUTLIER) cc_final: 0.6222 (t0) REVERT: x 58 ASP cc_start: 0.6387 (t70) cc_final: 0.5957 (t0) REVERT: x 83 TRP cc_start: 0.6431 (p-90) cc_final: 0.5892 (p-90) REVERT: y 96 MET cc_start: 0.4026 (OUTLIER) cc_final: 0.3472 (tmm) REVERT: y 169 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5979 (mt) REVERT: y 291 LYS cc_start: 0.6240 (pttp) cc_final: 0.5563 (mtmm) REVERT: 0 170 GLN cc_start: 0.7298 (mt0) cc_final: 0.6985 (mm110) REVERT: 1 32 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8218 (p) REVERT: 6 119 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7146 (tp30) REVERT: 7 43 MET cc_start: 0.7520 (ppp) cc_final: 0.6986 (ppp) REVERT: 9 105 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7321 (pttm) REVERT: D 295 TYR cc_start: 0.5647 (m-10) cc_final: 0.4893 (m-80) REVERT: H 97 ILE cc_start: 0.8251 (mt) cc_final: 0.7675 (tp) REVERT: H 141 GLU cc_start: 0.7243 (pp20) cc_final: 0.6864 (mm-30) REVERT: I 164 MET cc_start: 0.7206 (ptm) cc_final: 0.6249 (ppp) REVERT: I 166 ARG cc_start: 0.5934 (ptt-90) cc_final: 0.4459 (ptm-80) REVERT: J 79 GLU cc_start: 0.5566 (tt0) cc_final: 0.4252 (pm20) REVERT: J 170 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7111 (pp20) REVERT: L 42 ASP cc_start: 0.8037 (p0) cc_final: 0.7801 (p0) REVERT: O 120 MET cc_start: 0.7316 (mmm) cc_final: 0.7039 (mmt) REVERT: R 64 MET cc_start: 0.8586 (mmm) cc_final: 0.8316 (mmm) REVERT: U 46 MET cc_start: 0.8066 (mmm) cc_final: 0.7400 (mmt) REVERT: X 233 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: Y 155 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8326 (mm) REVERT: a 102 HIS cc_start: 0.6598 (t70) cc_final: 0.5630 (p-80) REVERT: d 248 PHE cc_start: 0.6614 (m-80) cc_final: 0.6292 (m-80) REVERT: d 261 MET cc_start: 0.6861 (ttp) cc_final: 0.6628 (ttp) REVERT: e 143 LYS cc_start: 0.7924 (tttt) cc_final: 0.7664 (pttt) REVERT: e 221 MET cc_start: 0.0658 (mtm) cc_final: 0.0447 (mtm) REVERT: e 224 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7363 (tm-30) REVERT: h 56 ARG cc_start: 0.5604 (ptt180) cc_final: 0.5260 (ttp80) REVERT: h 97 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7558 (mtpt) REVERT: h 135 GLN cc_start: 0.6886 (tp-100) cc_final: 0.6080 (mm-40) REVERT: j 103 ARG cc_start: 0.7930 (ptm-80) cc_final: 0.7121 (mtp-110) REVERT: j 104 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7652 (mtpt) REVERT: k 18 VAL cc_start: 0.7463 (t) cc_final: 0.7061 (m) REVERT: k 27 VAL cc_start: 0.7959 (m) cc_final: 0.7752 (t) REVERT: k 76 MET cc_start: 0.6807 (mtm) cc_final: 0.6137 (mtp) REVERT: k 92 SER cc_start: 0.6253 (p) cc_final: 0.5904 (m) REVERT: l 58 ASP cc_start: 0.1593 (OUTLIER) cc_final: 0.0974 (p0) REVERT: l 99 MET cc_start: 0.1714 (mmt) cc_final: 0.1234 (mmt) REVERT: l 113 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6726 (mp0) REVERT: l 134 LYS cc_start: 0.6050 (tttp) cc_final: 0.5568 (tptt) REVERT: m 51 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.5074 (tp) REVERT: m 58 LYS cc_start: 0.6938 (mttt) cc_final: 0.6495 (mmtm) REVERT: p 182 ASN cc_start: 0.8755 (m-40) cc_final: 0.8303 (m-40) REVERT: q 82 LEU cc_start: 0.8630 (tp) cc_final: 0.8255 (tt) REVERT: q 144 GLU cc_start: 0.8095 (tt0) cc_final: 0.7518 (tm-30) REVERT: q 155 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7581 (ptt-90) REVERT: r 190 THR cc_start: 0.8088 (m) cc_final: 0.7702 (p) outliers start: 242 outliers final: 173 residues processed: 1002 average time/residue: 0.9292 time to fit residues: 1623.5799 Evaluate side-chains 929 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 746 time to evaluate : 7.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 81 CYS Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 204 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain t residue 367 VAL Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 160 GLU Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 195 THR Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain w residue 111 ASP Chi-restraints excluded: chain x residue 100 ASN Chi-restraints excluded: chain x residue 196 CYS Chi-restraints excluded: chain x residue 210 ILE Chi-restraints excluded: chain y residue 96 MET Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 169 LEU Chi-restraints excluded: chain y residue 173 GLU Chi-restraints excluded: chain y residue 208 THR Chi-restraints excluded: chain y residue 223 LEU Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 175 ILE Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 77 LYS Chi-restraints excluded: chain 5 residue 151 ASP Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 379 ASP Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 187 VAL Chi-restraints excluded: chain 6 residue 280 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 218 THR Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain 9 residue 127 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 233 TYR Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 156 ASP Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 132 SER Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 115 LEU Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 169 THR Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 207 THR Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 233 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain b residue 40 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 89 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 84 SER Chi-restraints excluded: chain i residue 36 LEU Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain l residue 58 ASP Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 69 GLU Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 78 THR Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain p residue 132 GLU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 95 SER Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 50 GLU Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 116 GLU Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 148 ASP Chi-restraints excluded: chain s residue 178 ASP Chi-restraints excluded: chain s residue 243 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 977 optimal weight: 9.9990 chunk 744 optimal weight: 9.9990 chunk 513 optimal weight: 0.0770 chunk 109 optimal weight: 10.0000 chunk 472 optimal weight: 4.9990 chunk 664 optimal weight: 0.7980 chunk 993 optimal weight: 7.9990 chunk 1051 optimal weight: 8.9990 chunk 518 optimal weight: 10.0000 chunk 941 optimal weight: 3.9990 chunk 283 optimal weight: 20.0000 overall best weight: 3.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 299 HIS ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 165 GLN ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 207 HIS 7 255 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS b 123 ASN ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 155 ASN c 222 GLN d 149 HIS d 235 GLN h 99 ASN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN k 46 ASN ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 116061 Z= 0.257 Angle : 0.570 17.869 164252 Z= 0.287 Chirality : 0.038 0.258 19153 Planarity : 0.004 0.122 15513 Dihedral : 19.663 179.572 33510 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.54 % Allowed : 10.01 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.64 (0.09), residues: 9449 helix: 1.04 (0.09), residues: 3294 sheet: -0.08 (0.14), residues: 1303 loop : 0.29 (0.09), residues: 4852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP t 318 HIS 0.015 0.001 HIS d 193 PHE 0.029 0.001 PHE y 316 TYR 0.026 0.001 TYR 5 176 ARG 0.016 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 793 time to evaluate : 6.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 229 MET cc_start: 0.3633 (ttm) cc_final: 0.3144 (ttm) REVERT: t 361 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6131 (m-30) REVERT: t 365 GLN cc_start: 0.3946 (OUTLIER) cc_final: 0.3283 (pt0) REVERT: u 118 MET cc_start: 0.5582 (mmm) cc_final: 0.5248 (mmm) REVERT: u 126 ILE cc_start: 0.7777 (mp) cc_final: 0.7566 (mp) REVERT: u 179 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8008 (mp) REVERT: u 189 GLU cc_start: 0.6482 (mt-10) cc_final: 0.6243 (mp0) REVERT: v 40 ARG cc_start: 0.7046 (mtm180) cc_final: 0.6162 (tpm170) REVERT: x 58 ASP cc_start: 0.6292 (t70) cc_final: 0.5851 (t0) REVERT: x 83 TRP cc_start: 0.6283 (p-90) cc_final: 0.5772 (p-90) REVERT: x 349 MET cc_start: 0.7069 (mmm) cc_final: 0.6816 (ttt) REVERT: x 380 MET cc_start: 0.8074 (pmm) cc_final: 0.7822 (pmm) REVERT: y 96 MET cc_start: 0.3999 (ttp) cc_final: 0.3380 (ptp) REVERT: y 247 ASP cc_start: 0.7003 (t0) cc_final: 0.6797 (t0) REVERT: y 291 LYS cc_start: 0.6287 (pttp) cc_final: 0.5623 (mtmm) REVERT: 0 170 GLN cc_start: 0.7338 (mt0) cc_final: 0.7002 (mm110) REVERT: 1 32 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8111 (p) REVERT: 6 119 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7101 (tp30) REVERT: 7 43 MET cc_start: 0.7156 (ppp) cc_final: 0.5546 (mmm) REVERT: 7 142 TYR cc_start: 0.7134 (t80) cc_final: 0.6891 (t80) REVERT: 9 80 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6748 (tm-30) REVERT: 9 105 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7244 (ttpp) REVERT: D 275 TRP cc_start: 0.7731 (t60) cc_final: 0.7489 (t60) REVERT: D 292 MET cc_start: 0.7807 (mmm) cc_final: 0.7493 (mmp) REVERT: E 219 MET cc_start: 0.8996 (ttm) cc_final: 0.8756 (tpp) REVERT: F 103 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: H 91 LYS cc_start: 0.6908 (mttt) cc_final: 0.6522 (mttp) REVERT: H 97 ILE cc_start: 0.8223 (mt) cc_final: 0.7664 (tp) REVERT: H 141 GLU cc_start: 0.7109 (pp20) cc_final: 0.6790 (mm-30) REVERT: I 164 MET cc_start: 0.7189 (ptm) cc_final: 0.6186 (ppp) REVERT: I 166 ARG cc_start: 0.5922 (ptt-90) cc_final: 0.4320 (ttp80) REVERT: J 51 LYS cc_start: 0.5636 (mttt) cc_final: 0.5147 (mmtp) REVERT: J 79 GLU cc_start: 0.5618 (tt0) cc_final: 0.4262 (pm20) REVERT: J 170 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7131 (pp20) REVERT: L 42 ASP cc_start: 0.7934 (p0) cc_final: 0.7724 (p0) REVERT: M 228 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8013 (mtmt) REVERT: Q 99 MET cc_start: 0.8766 (mtm) cc_final: 0.8450 (mtm) REVERT: R 64 MET cc_start: 0.8510 (mmm) cc_final: 0.8235 (mmm) REVERT: U 46 MET cc_start: 0.8060 (mmm) cc_final: 0.7324 (mmt) REVERT: V 66 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: V 78 GLN cc_start: 0.4991 (OUTLIER) cc_final: 0.4218 (tm-30) REVERT: X 233 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: Y 155 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8241 (mm) REVERT: Y 157 GLN cc_start: 0.8330 (mm110) cc_final: 0.7719 (mm-40) REVERT: a 102 HIS cc_start: 0.6584 (t70) cc_final: 0.5597 (p-80) REVERT: c 155 ASN cc_start: 0.7044 (OUTLIER) cc_final: 0.6814 (t0) REVERT: d 57 MET cc_start: 0.4452 (tmm) cc_final: 0.2866 (mpp) REVERT: d 248 PHE cc_start: 0.6486 (m-80) cc_final: 0.6139 (m-80) REVERT: e 143 LYS cc_start: 0.7920 (tttt) cc_final: 0.7675 (pttt) REVERT: e 224 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7387 (tm-30) REVERT: h 56 ARG cc_start: 0.5572 (ptt180) cc_final: 0.5205 (ttp80) REVERT: h 137 ARG cc_start: 0.6402 (ptt-90) cc_final: 0.5694 (ptt-90) REVERT: j 103 ARG cc_start: 0.8060 (ptm-80) cc_final: 0.7172 (mtp-110) REVERT: j 104 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7647 (mptt) REVERT: k 18 VAL cc_start: 0.7419 (t) cc_final: 0.6995 (m) REVERT: k 27 VAL cc_start: 0.7923 (m) cc_final: 0.7716 (t) REVERT: k 76 MET cc_start: 0.6585 (mtm) cc_final: 0.5938 (mtp) REVERT: k 92 SER cc_start: 0.6293 (p) cc_final: 0.5961 (m) REVERT: l 58 ASP cc_start: 0.1560 (OUTLIER) cc_final: 0.0951 (p0) REVERT: l 99 MET cc_start: 0.1723 (mmt) cc_final: 0.1184 (mmt) REVERT: l 113 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6768 (mp0) REVERT: l 134 LYS cc_start: 0.5916 (tttp) cc_final: 0.5479 (tptt) REVERT: m 51 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5499 (mm) REVERT: m 58 LYS cc_start: 0.6969 (mttt) cc_final: 0.6440 (mmtm) REVERT: p 184 ASN cc_start: 0.7740 (m-40) cc_final: 0.7532 (m-40) REVERT: p 188 LEU cc_start: 0.7988 (tt) cc_final: 0.7400 (tp) REVERT: q 82 LEU cc_start: 0.8621 (tp) cc_final: 0.8215 (tt) REVERT: q 144 GLU cc_start: 0.8049 (tt0) cc_final: 0.7489 (tm-30) REVERT: q 155 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7635 (ptt-90) REVERT: r 190 THR cc_start: 0.8180 (m) cc_final: 0.7796 (p) outliers start: 214 outliers final: 156 residues processed: 947 average time/residue: 0.9304 time to fit residues: 1540.1195 Evaluate side-chains 907 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 738 time to evaluate : 7.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 73 VAL Chi-restraints excluded: chain t residue 81 CYS Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 204 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 195 THR Chi-restraints excluded: chain x residue 188 THR Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 173 GLU Chi-restraints excluded: chain y residue 223 LEU Chi-restraints excluded: chain y residue 261 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 175 ILE Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 77 LYS Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 379 ASP Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 187 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 280 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 91 CYS Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain 9 residue 127 LEU Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 80 ILE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 132 SER Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 233 GLU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain b residue 40 SER Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 89 ILE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 155 ASN Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 240 THR Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 69 ARG Chi-restraints excluded: chain h residue 84 SER Chi-restraints excluded: chain i residue 36 LEU Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain l residue 58 ASP Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 78 THR Chi-restraints excluded: chain p residue 132 GLU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 50 GLU Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 116 GLU Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 178 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 875 optimal weight: 0.0570 chunk 596 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 783 optimal weight: 2.9990 chunk 433 optimal weight: 5.9990 chunk 897 optimal weight: 7.9990 chunk 726 optimal weight: 7.9990 chunk 1 optimal weight: 30.0000 chunk 537 optimal weight: 3.9990 chunk 943 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 299 HIS t 314 GLN ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 98 GLN ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 354 GLN 7 207 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 ASN N 178 GLN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 116061 Z= 0.264 Angle : 0.570 17.755 164252 Z= 0.286 Chirality : 0.038 0.361 19153 Planarity : 0.004 0.122 15513 Dihedral : 19.650 179.738 33510 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.78 % Allowed : 10.55 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.63 (0.09), residues: 9449 helix: 1.10 (0.09), residues: 3293 sheet: -0.14 (0.14), residues: 1314 loop : 0.25 (0.09), residues: 4842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP t 318 HIS 0.015 0.001 HIS t 299 PHE 0.040 0.002 PHE y 316 TYR 0.023 0.002 TYR u 146 ARG 0.006 0.000 ARG 6 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 771 time to evaluate : 7.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 229 MET cc_start: 0.4275 (ttm) cc_final: 0.3724 (ttm) REVERT: t 361 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6028 (m-30) REVERT: t 365 GLN cc_start: 0.4026 (OUTLIER) cc_final: 0.3301 (pt0) REVERT: t 379 GLU cc_start: 0.6063 (mt-10) cc_final: 0.5404 (pp20) REVERT: u 118 MET cc_start: 0.5574 (mmm) cc_final: 0.5298 (mmm) REVERT: u 126 ILE cc_start: 0.7828 (mp) cc_final: 0.7477 (mt) REVERT: u 160 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: u 179 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7903 (mp) REVERT: u 180 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6388 (mpp) REVERT: v 40 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6161 (tpm170) REVERT: w 111 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6116 (t0) REVERT: x 58 ASP cc_start: 0.6295 (t70) cc_final: 0.5859 (t0) REVERT: x 83 TRP cc_start: 0.6344 (p-90) cc_final: 0.5831 (p-90) REVERT: x 349 MET cc_start: 0.7207 (mmm) cc_final: 0.6958 (ttt) REVERT: x 380 MET cc_start: 0.8112 (pmm) cc_final: 0.7895 (pmm) REVERT: y 96 MET cc_start: 0.3785 (OUTLIER) cc_final: 0.3447 (tmm) REVERT: y 100 LEU cc_start: 0.2248 (mt) cc_final: 0.1699 (tp) REVERT: y 247 ASP cc_start: 0.7041 (t0) cc_final: 0.6809 (t0) REVERT: y 291 LYS cc_start: 0.6299 (pttp) cc_final: 0.5649 (mtmm) REVERT: 0 170 GLN cc_start: 0.7396 (mt0) cc_final: 0.7033 (mm110) REVERT: 1 32 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8119 (p) REVERT: 7 142 TYR cc_start: 0.7156 (t80) cc_final: 0.6899 (t80) REVERT: 9 76 TYR cc_start: 0.7686 (m-80) cc_final: 0.7007 (m-80) REVERT: 9 105 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7257 (ttpp) REVERT: D 275 TRP cc_start: 0.7740 (t60) cc_final: 0.7494 (t60) REVERT: D 292 MET cc_start: 0.7741 (mmm) cc_final: 0.7263 (mmp) REVERT: D 295 TYR cc_start: 0.5710 (m-10) cc_final: 0.4999 (m-80) REVERT: F 74 GLN cc_start: 0.8025 (mp10) cc_final: 0.7491 (mp10) REVERT: H 97 ILE cc_start: 0.8223 (mt) cc_final: 0.7687 (tp) REVERT: H 141 GLU cc_start: 0.7025 (pp20) cc_final: 0.6754 (mm-30) REVERT: I 164 MET cc_start: 0.7194 (ptm) cc_final: 0.6255 (ppp) REVERT: I 166 ARG cc_start: 0.5918 (ptt-90) cc_final: 0.4269 (ttp80) REVERT: J 51 LYS cc_start: 0.5624 (mttt) cc_final: 0.5152 (mmtp) REVERT: J 79 GLU cc_start: 0.5657 (tt0) cc_final: 0.4281 (pm20) REVERT: J 127 ASP cc_start: 0.4689 (t0) cc_final: 0.3780 (p0) REVERT: J 170 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7136 (pp20) REVERT: L 42 ASP cc_start: 0.8055 (p0) cc_final: 0.7839 (p0) REVERT: O 67 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7267 (p0) REVERT: Q 99 MET cc_start: 0.8721 (mtm) cc_final: 0.8331 (mtm) REVERT: S 87 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7953 (mm) REVERT: U 46 MET cc_start: 0.8023 (mmm) cc_final: 0.7290 (mmt) REVERT: V 66 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: X 233 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6556 (tm-30) REVERT: Y 153 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8513 (tt) REVERT: Y 155 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8165 (mm) REVERT: Y 157 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7728 (mm110) REVERT: a 102 HIS cc_start: 0.6757 (t70) cc_final: 0.5600 (p-80) REVERT: d 202 MET cc_start: 0.1493 (ppp) cc_final: 0.0930 (ppp) REVERT: d 232 MET cc_start: 0.6933 (ttp) cc_final: 0.6614 (ttp) REVERT: d 248 PHE cc_start: 0.6465 (m-80) cc_final: 0.6130 (m-80) REVERT: e 224 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7399 (tm-30) REVERT: h 56 ARG cc_start: 0.5446 (ptt180) cc_final: 0.5026 (ttp80) REVERT: h 136 ASP cc_start: 0.5460 (t0) cc_final: 0.5237 (t0) REVERT: i 38 LEU cc_start: 0.7917 (tp) cc_final: 0.7691 (tt) REVERT: j 100 GLU cc_start: 0.8044 (pp20) cc_final: 0.7095 (tm-30) REVERT: j 103 ARG cc_start: 0.7909 (ptm-80) cc_final: 0.7519 (mtp-110) REVERT: j 104 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7572 (mtpt) REVERT: k 11 ARG cc_start: 0.5158 (tpp-160) cc_final: 0.4781 (tpm170) REVERT: k 18 VAL cc_start: 0.7378 (t) cc_final: 0.6947 (m) REVERT: k 27 VAL cc_start: 0.7883 (m) cc_final: 0.7674 (t) REVERT: k 76 MET cc_start: 0.6574 (mtm) cc_final: 0.5959 (mtp) REVERT: k 92 SER cc_start: 0.6245 (p) cc_final: 0.5890 (m) REVERT: l 58 ASP cc_start: 0.1405 (OUTLIER) cc_final: 0.0906 (p0) REVERT: l 73 MET cc_start: 0.3301 (mmm) cc_final: 0.3009 (mmm) REVERT: l 99 MET cc_start: 0.1824 (mmt) cc_final: 0.1211 (mmt) REVERT: l 113 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6752 (mp0) REVERT: l 134 LYS cc_start: 0.6100 (tttp) cc_final: 0.5632 (tptt) REVERT: m 51 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5510 (mm) REVERT: m 58 LYS cc_start: 0.6801 (mttt) cc_final: 0.6321 (mmtm) REVERT: q 82 LEU cc_start: 0.8661 (tp) cc_final: 0.8261 (tt) REVERT: q 142 ASN cc_start: 0.8545 (m-40) cc_final: 0.8133 (p0) REVERT: q 155 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7692 (ptt-90) REVERT: r 190 THR cc_start: 0.8165 (m) cc_final: 0.7770 (p) outliers start: 234 outliers final: 177 residues processed: 936 average time/residue: 0.9507 time to fit residues: 1560.2459 Evaluate side-chains 926 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 733 time to evaluate : 7.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 73 VAL Chi-restraints excluded: chain t residue 81 CYS Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 204 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain t residue 230 VAL Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain t residue 367 VAL Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 160 GLU Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain u residue 195 THR Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain w residue 111 ASP Chi-restraints excluded: chain x residue 233 VAL Chi-restraints excluded: chain y residue 96 MET Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 180 LEU Chi-restraints excluded: chain y residue 217 HIS Chi-restraints excluded: chain y residue 223 LEU Chi-restraints excluded: chain y residue 261 ILE Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 175 ILE Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 77 LYS Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 379 ASP Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 187 VAL Chi-restraints excluded: chain 6 residue 276 ASP Chi-restraints excluded: chain 6 residue 280 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 218 THR Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 9 residue 127 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 80 ILE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 228 LYS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 121 MET Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 132 SER Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 115 LEU Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 169 THR Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 233 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 89 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 84 SER Chi-restraints excluded: chain i residue 36 LEU Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain l residue 58 ASP Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 74 ILE Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 78 THR Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 132 GLU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 95 SER Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 50 GLU Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 116 GLU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 178 ASP Chi-restraints excluded: chain s residue 243 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 353 optimal weight: 10.0000 chunk 947 optimal weight: 5.9990 chunk 207 optimal weight: 0.3980 chunk 617 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 chunk 1052 optimal weight: 2.9990 chunk 873 optimal weight: 6.9990 chunk 487 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 552 optimal weight: 0.9980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 299 HIS t 314 GLN ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 314 HIS x 316 GLN ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 354 GLN 7 207 HIS ** 7 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 ASN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 196 GLN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 143 GLN ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 116061 Z= 0.253 Angle : 0.563 17.764 164252 Z= 0.282 Chirality : 0.038 0.257 19153 Planarity : 0.004 0.120 15513 Dihedral : 19.642 179.308 33510 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.86 % Allowed : 11.08 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.63 (0.09), residues: 9449 helix: 1.14 (0.09), residues: 3303 sheet: -0.20 (0.14), residues: 1350 loop : 0.23 (0.09), residues: 4796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP t 318 HIS 0.014 0.001 HIS t 299 PHE 0.043 0.001 PHE y 316 TYR 0.026 0.001 TYR 8 124 ARG 0.007 0.000 ARG 6 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 763 time to evaluate : 6.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 229 MET cc_start: 0.4351 (ttm) cc_final: 0.3909 (ttm) REVERT: t 361 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6049 (m-30) REVERT: t 365 GLN cc_start: 0.3975 (OUTLIER) cc_final: 0.3290 (pt0) REVERT: t 379 GLU cc_start: 0.5965 (mt-10) cc_final: 0.5290 (pp20) REVERT: u 118 MET cc_start: 0.5664 (mmm) cc_final: 0.5463 (mmm) REVERT: u 126 ILE cc_start: 0.7872 (mp) cc_final: 0.7655 (mp) REVERT: u 160 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: u 179 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7864 (mp) REVERT: u 189 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: v 40 ARG cc_start: 0.7083 (mtm180) cc_final: 0.6347 (tpm170) REVERT: w 111 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6193 (t0) REVERT: x 58 ASP cc_start: 0.6326 (t70) cc_final: 0.5893 (t0) REVERT: x 83 TRP cc_start: 0.6334 (p-90) cc_final: 0.5833 (p-90) REVERT: x 349 MET cc_start: 0.7268 (mmm) cc_final: 0.7030 (ttt) REVERT: x 380 MET cc_start: 0.8045 (pmm) cc_final: 0.7822 (pmm) REVERT: y 96 MET cc_start: 0.3911 (OUTLIER) cc_final: 0.3613 (tmm) REVERT: y 100 LEU cc_start: 0.2156 (mt) cc_final: 0.1612 (tp) REVERT: y 247 ASP cc_start: 0.7327 (t0) cc_final: 0.7078 (t0) REVERT: y 291 LYS cc_start: 0.6308 (pttp) cc_final: 0.5654 (mtmm) REVERT: 0 170 GLN cc_start: 0.7313 (mt0) cc_final: 0.6991 (mm110) REVERT: 1 32 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8126 (p) REVERT: 1 64 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.8024 (m) REVERT: 7 81 MET cc_start: 0.7898 (mmm) cc_final: 0.7296 (mmt) REVERT: 7 142 TYR cc_start: 0.7153 (t80) cc_final: 0.6943 (t80) REVERT: 9 76 TYR cc_start: 0.7610 (m-80) cc_final: 0.6907 (m-80) REVERT: 9 105 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7318 (ttpp) REVERT: D 275 TRP cc_start: 0.7739 (t60) cc_final: 0.7488 (t60) REVERT: D 292 MET cc_start: 0.7889 (mmm) cc_final: 0.7530 (mmp) REVERT: D 295 TYR cc_start: 0.5593 (m-10) cc_final: 0.4945 (m-80) REVERT: E 77 LEU cc_start: 0.7564 (mm) cc_final: 0.6923 (tt) REVERT: I 164 MET cc_start: 0.7191 (ptm) cc_final: 0.6203 (ppp) REVERT: I 166 ARG cc_start: 0.5887 (ptt-90) cc_final: 0.4353 (ttp80) REVERT: J 51 LYS cc_start: 0.5547 (mttt) cc_final: 0.5084 (mmtp) REVERT: J 79 GLU cc_start: 0.5538 (tt0) cc_final: 0.4195 (pm20) REVERT: J 115 LYS cc_start: 0.6931 (mttt) cc_final: 0.6647 (ttpt) REVERT: J 127 ASP cc_start: 0.4684 (t0) cc_final: 0.3798 (p0) REVERT: J 170 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7142 (pp20) REVERT: R 64 MET cc_start: 0.8464 (mmm) cc_final: 0.8244 (mmm) REVERT: U 46 MET cc_start: 0.8031 (mmm) cc_final: 0.7324 (mmt) REVERT: V 66 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: V 165 ILE cc_start: 0.3915 (OUTLIER) cc_final: 0.3348 (mm) REVERT: X 233 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: Y 153 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8487 (tt) REVERT: Y 155 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8117 (mm) REVERT: Z 80 TYR cc_start: 0.8618 (p90) cc_final: 0.8412 (p90) REVERT: d 248 PHE cc_start: 0.6473 (m-80) cc_final: 0.6122 (m-80) REVERT: e 224 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7419 (tm-30) REVERT: h 56 ARG cc_start: 0.5478 (ptt180) cc_final: 0.5021 (ttp80) REVERT: h 136 ASP cc_start: 0.5731 (t0) cc_final: 0.5509 (t0) REVERT: i 38 LEU cc_start: 0.7997 (tp) cc_final: 0.7758 (mm) REVERT: k 11 ARG cc_start: 0.5115 (tpp-160) cc_final: 0.4761 (tpm170) REVERT: k 27 VAL cc_start: 0.7932 (m) cc_final: 0.7709 (t) REVERT: k 76 MET cc_start: 0.6354 (mtm) cc_final: 0.5740 (mtp) REVERT: k 92 SER cc_start: 0.6227 (p) cc_final: 0.5871 (m) REVERT: l 58 ASP cc_start: 0.1457 (OUTLIER) cc_final: 0.0873 (p0) REVERT: l 73 MET cc_start: 0.3312 (mmm) cc_final: 0.2948 (mmm) REVERT: l 99 MET cc_start: 0.1738 (mmt) cc_final: 0.1105 (mmt) REVERT: l 113 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6755 (mp0) REVERT: l 134 LYS cc_start: 0.6095 (tttp) cc_final: 0.5668 (tptt) REVERT: m 51 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5666 (mm) REVERT: m 58 LYS cc_start: 0.6722 (mttt) cc_final: 0.6203 (mmtm) REVERT: q 155 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7650 (ptt-90) REVERT: r 190 THR cc_start: 0.8218 (m) cc_final: 0.7780 (p) outliers start: 241 outliers final: 186 residues processed: 940 average time/residue: 0.9263 time to fit residues: 1530.9173 Evaluate side-chains 921 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 719 time to evaluate : 7.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 71 TYR Chi-restraints excluded: chain t residue 73 VAL Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 204 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 160 GLU Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 189 GLU Chi-restraints excluded: chain u residue 195 THR Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain w residue 111 ASP Chi-restraints excluded: chain x residue 163 LEU Chi-restraints excluded: chain x residue 188 THR Chi-restraints excluded: chain x residue 233 VAL Chi-restraints excluded: chain y residue 96 MET Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 180 LEU Chi-restraints excluded: chain y residue 208 THR Chi-restraints excluded: chain y residue 217 HIS Chi-restraints excluded: chain y residue 223 LEU Chi-restraints excluded: chain y residue 276 THR Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 175 ILE Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 64 SER Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 372 ASN Chi-restraints excluded: chain 5 residue 379 ASP Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 187 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 276 ASP Chi-restraints excluded: chain 6 residue 280 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 218 THR Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 112 ASP Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain 9 residue 127 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 80 ILE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 148 THR Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 127 ASN Chi-restraints excluded: chain T residue 132 SER Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 94 HIS Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 165 ILE Chi-restraints excluded: chain V residue 169 THR Chi-restraints excluded: chain V residue 171 ILE Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 233 GLU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 89 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain d residue 134 ILE Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 240 THR Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 84 SER Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain l residue 58 ASP Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 74 ILE Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 78 THR Chi-restraints excluded: chain p residue 132 GLU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 95 SER Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 46 THR Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 116 GLU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 178 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 404 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 1014 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 599 optimal weight: 3.9990 chunk 768 optimal weight: 9.9990 chunk 595 optimal weight: 2.9990 chunk 886 optimal weight: 7.9990 chunk 587 optimal weight: 5.9990 chunk 1048 optimal weight: 7.9990 chunk 656 optimal weight: 0.4980 chunk 639 optimal weight: 4.9990 chunk 484 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 299 HIS t 314 GLN ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 316 GLN ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 358 GLN ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 207 HIS ** 7 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 ASN K 74 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 116061 Z= 0.164 Angle : 0.525 17.911 164252 Z= 0.262 Chirality : 0.036 0.235 19153 Planarity : 0.004 0.116 15513 Dihedral : 19.593 179.860 33510 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.38 % Allowed : 11.68 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.79 (0.09), residues: 9449 helix: 1.30 (0.09), residues: 3306 sheet: -0.14 (0.14), residues: 1351 loop : 0.31 (0.09), residues: 4792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP l 127 HIS 0.018 0.001 HIS t 299 PHE 0.023 0.001 PHE y 316 TYR 0.028 0.001 TYR 8 124 ARG 0.006 0.000 ARG 6 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 784 time to evaluate : 7.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 229 MET cc_start: 0.4346 (ttm) cc_final: 0.3647 (ttm) REVERT: t 330 MET cc_start: 0.4448 (ppp) cc_final: 0.2111 (tpp) REVERT: t 365 GLN cc_start: 0.4062 (OUTLIER) cc_final: 0.3235 (pt0) REVERT: t 379 GLU cc_start: 0.5809 (mt-10) cc_final: 0.5211 (pp20) REVERT: u 126 ILE cc_start: 0.7855 (mp) cc_final: 0.7638 (mp) REVERT: u 160 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: u 179 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7887 (mp) REVERT: u 189 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5965 (mp0) REVERT: v 40 ARG cc_start: 0.7072 (mtm180) cc_final: 0.6331 (tpm170) REVERT: w 111 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6267 (t0) REVERT: w 122 MET cc_start: 0.6857 (mtt) cc_final: 0.5813 (mmp) REVERT: x 58 ASP cc_start: 0.6348 (t70) cc_final: 0.5915 (t0) REVERT: x 83 TRP cc_start: 0.6359 (p-90) cc_final: 0.5904 (p-90) REVERT: x 241 TRP cc_start: 0.6623 (m100) cc_final: 0.5823 (m100) REVERT: x 349 MET cc_start: 0.7223 (mmm) cc_final: 0.7009 (ttt) REVERT: x 380 MET cc_start: 0.8039 (pmm) cc_final: 0.7806 (pmm) REVERT: y 96 MET cc_start: 0.4022 (OUTLIER) cc_final: 0.3701 (tmm) REVERT: y 100 LEU cc_start: 0.2097 (mt) cc_final: 0.1581 (tp) REVERT: y 247 ASP cc_start: 0.7332 (t0) cc_final: 0.7079 (t0) REVERT: y 291 LYS cc_start: 0.6353 (pttp) cc_final: 0.5691 (mtmm) REVERT: 0 170 GLN cc_start: 0.7293 (mt0) cc_final: 0.6975 (mm110) REVERT: 7 81 MET cc_start: 0.7790 (mmm) cc_final: 0.7285 (mmt) REVERT: 7 115 MET cc_start: 0.8422 (mmm) cc_final: 0.7950 (mmm) REVERT: 7 142 TYR cc_start: 0.7162 (t80) cc_final: 0.6936 (t80) REVERT: 9 76 TYR cc_start: 0.7622 (m-80) cc_final: 0.6928 (m-80) REVERT: 9 105 LYS cc_start: 0.7642 (mmtt) cc_final: 0.7335 (ttpp) REVERT: D 275 TRP cc_start: 0.7707 (t60) cc_final: 0.7457 (t60) REVERT: D 292 MET cc_start: 0.7899 (mmm) cc_final: 0.7686 (mmp) REVERT: D 295 TYR cc_start: 0.5549 (m-80) cc_final: 0.4771 (m-80) REVERT: E 77 LEU cc_start: 0.7704 (mm) cc_final: 0.6984 (tt) REVERT: E 106 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7322 (mtt) REVERT: H 145 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7148 (pp) REVERT: I 164 MET cc_start: 0.7156 (ptm) cc_final: 0.6141 (ppp) REVERT: I 166 ARG cc_start: 0.5842 (ptt-90) cc_final: 0.4353 (ttp80) REVERT: J 51 LYS cc_start: 0.5641 (mttt) cc_final: 0.5285 (mmtp) REVERT: J 79 GLU cc_start: 0.5645 (tt0) cc_final: 0.4280 (pm20) REVERT: J 115 LYS cc_start: 0.6929 (mttt) cc_final: 0.6640 (ttpt) REVERT: J 118 TYR cc_start: 0.5993 (t80) cc_final: 0.5695 (t80) REVERT: J 127 ASP cc_start: 0.4613 (t0) cc_final: 0.3774 (p0) REVERT: J 170 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7139 (pp20) REVERT: K 121 MET cc_start: 0.8309 (mtt) cc_final: 0.8052 (mtt) REVERT: M 111 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6606 (p0) REVERT: R 64 MET cc_start: 0.8486 (mmm) cc_final: 0.8240 (mmm) REVERT: U 46 MET cc_start: 0.7995 (mmm) cc_final: 0.7041 (mmm) REVERT: V 165 ILE cc_start: 0.3766 (OUTLIER) cc_final: 0.3332 (mt) REVERT: W 57 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: X 233 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: Y 153 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8447 (tt) REVERT: Y 155 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8034 (mm) REVERT: d 202 MET cc_start: 0.1486 (ppp) cc_final: 0.0757 (ppp) REVERT: d 248 PHE cc_start: 0.6446 (m-80) cc_final: 0.6080 (m-80) REVERT: d 261 MET cc_start: 0.7008 (ptt) cc_final: 0.6508 (ptt) REVERT: e 224 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7453 (tm-30) REVERT: g 123 ASP cc_start: 0.7447 (t0) cc_final: 0.7040 (t0) REVERT: h 56 ARG cc_start: 0.5436 (ptt180) cc_final: 0.5004 (ttp80) REVERT: h 95 ARG cc_start: 0.7637 (mtp85) cc_final: 0.7247 (mmp80) REVERT: h 136 ASP cc_start: 0.5584 (t0) cc_final: 0.5376 (t0) REVERT: i 38 LEU cc_start: 0.8030 (tp) cc_final: 0.7796 (mm) REVERT: k 11 ARG cc_start: 0.5102 (tpp-160) cc_final: 0.4687 (tpm170) REVERT: k 76 MET cc_start: 0.6592 (mtm) cc_final: 0.6223 (mtp) REVERT: k 92 SER cc_start: 0.6219 (p) cc_final: 0.5857 (m) REVERT: l 58 ASP cc_start: 0.1403 (OUTLIER) cc_final: 0.0836 (p0) REVERT: l 73 MET cc_start: 0.3660 (mmm) cc_final: 0.2987 (mmm) REVERT: l 99 MET cc_start: 0.1618 (mmt) cc_final: 0.1028 (mmt) REVERT: l 113 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6828 (mp0) REVERT: l 127 TRP cc_start: 0.5426 (m-10) cc_final: 0.5171 (m-10) REVERT: l 134 LYS cc_start: 0.6017 (tttp) cc_final: 0.5550 (tptt) REVERT: m 51 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5605 (mm) REVERT: m 58 LYS cc_start: 0.6777 (mttt) cc_final: 0.6291 (mmtm) REVERT: p 136 THR cc_start: 0.7275 (m) cc_final: 0.6626 (t) REVERT: p 188 LEU cc_start: 0.8121 (tt) cc_final: 0.7426 (tp) REVERT: q 82 LEU cc_start: 0.8670 (tp) cc_final: 0.8367 (tt) REVERT: q 142 ASN cc_start: 0.8540 (m-40) cc_final: 0.8144 (p0) REVERT: q 155 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7723 (ptt-90) REVERT: r 190 THR cc_start: 0.8212 (m) cc_final: 0.7776 (p) outliers start: 201 outliers final: 151 residues processed: 925 average time/residue: 0.9387 time to fit residues: 1526.9886 Evaluate side-chains 912 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 745 time to evaluate : 7.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 71 TYR Chi-restraints excluded: chain t residue 73 VAL Chi-restraints excluded: chain t residue 84 ASN Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 204 VAL Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain u residue 160 GLU Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 187 ILE Chi-restraints excluded: chain u residue 189 GLU Chi-restraints excluded: chain u residue 195 THR Chi-restraints excluded: chain u residue 200 ASP Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain w residue 111 ASP Chi-restraints excluded: chain x residue 163 LEU Chi-restraints excluded: chain x residue 233 VAL Chi-restraints excluded: chain y residue 96 MET Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 180 LEU Chi-restraints excluded: chain y residue 217 HIS Chi-restraints excluded: chain y residue 223 LEU Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 175 ILE Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 372 ASN Chi-restraints excluded: chain 5 residue 379 ASP Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 187 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 276 ASP Chi-restraints excluded: chain 6 residue 280 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 93 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 218 THR Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain 9 residue 127 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 132 SER Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 165 ILE Chi-restraints excluded: chain V residue 169 THR Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 233 GLU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 89 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain d residue 134 ILE Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 240 THR Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain l residue 58 ASP Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 74 ILE Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 243 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 648 optimal weight: 0.9990 chunk 418 optimal weight: 20.0000 chunk 626 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 666 optimal weight: 9.9990 chunk 714 optimal weight: 9.9990 chunk 518 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 824 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 314 GLN ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 316 GLN ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 354 GLN 7 207 HIS ** 7 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN F 184 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN J 47 ASN K 74 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 116061 Z= 0.392 Angle : 0.649 17.465 164252 Z= 0.324 Chirality : 0.041 0.228 19153 Planarity : 0.005 0.124 15513 Dihedral : 19.673 178.632 33510 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.82 % Allowed : 11.80 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.44 (0.09), residues: 9449 helix: 0.99 (0.09), residues: 3297 sheet: -0.25 (0.14), residues: 1323 loop : 0.08 (0.09), residues: 4829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP t 318 HIS 0.013 0.001 HIS d 193 PHE 0.023 0.002 PHE 5 60 TYR 0.036 0.002 TYR 7 181 ARG 0.007 0.001 ARG h 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 752 time to evaluate : 7.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 229 MET cc_start: 0.4263 (ttm) cc_final: 0.3552 (ttm) REVERT: t 330 MET cc_start: 0.4300 (ppp) cc_final: 0.2051 (tpp) REVERT: t 361 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6082 (m-30) REVERT: t 365 GLN cc_start: 0.3930 (OUTLIER) cc_final: 0.3016 (pt0) REVERT: u 126 ILE cc_start: 0.7998 (mp) cc_final: 0.7495 (mt) REVERT: u 179 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8007 (mp) REVERT: u 180 MET cc_start: 0.6988 (ptp) cc_final: 0.6459 (mpp) REVERT: u 189 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: v 40 ARG cc_start: 0.7093 (mtm180) cc_final: 0.6164 (tpt170) REVERT: x 58 ASP cc_start: 0.6539 (t70) cc_final: 0.6118 (t0) REVERT: x 83 TRP cc_start: 0.6350 (p-90) cc_final: 0.5837 (p-90) REVERT: x 241 TRP cc_start: 0.6592 (m100) cc_final: 0.5793 (m100) REVERT: x 349 MET cc_start: 0.7226 (mmm) cc_final: 0.7019 (ttt) REVERT: x 380 MET cc_start: 0.8128 (pmm) cc_final: 0.7885 (pmm) REVERT: y 96 MET cc_start: 0.3768 (OUTLIER) cc_final: 0.3405 (tmm) REVERT: y 100 LEU cc_start: 0.2204 (mt) cc_final: 0.1929 (mt) REVERT: y 247 ASP cc_start: 0.7388 (t0) cc_final: 0.7137 (t0) REVERT: y 291 LYS cc_start: 0.6328 (pttp) cc_final: 0.5707 (mtmm) REVERT: 0 170 GLN cc_start: 0.7485 (mt0) cc_final: 0.7102 (mm110) REVERT: 1 32 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8111 (p) REVERT: 7 81 MET cc_start: 0.7977 (mmm) cc_final: 0.7442 (mmt) REVERT: 7 115 MET cc_start: 0.8467 (mmm) cc_final: 0.7992 (mmm) REVERT: 7 142 TYR cc_start: 0.7228 (t80) cc_final: 0.6903 (t80) REVERT: 7 323 MET cc_start: 0.6542 (mmm) cc_final: 0.5404 (mmt) REVERT: 9 76 TYR cc_start: 0.7560 (m-80) cc_final: 0.6989 (m-80) REVERT: 9 102 LYS cc_start: 0.7534 (tttt) cc_final: 0.7242 (mptt) REVERT: 9 105 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7370 (ttpp) REVERT: D 292 MET cc_start: 0.8043 (mmm) cc_final: 0.7836 (mmp) REVERT: D 295 TYR cc_start: 0.5610 (m-80) cc_final: 0.4777 (m-80) REVERT: E 77 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.6846 (tt) REVERT: F 103 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7330 (mm-40) REVERT: H 145 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7337 (pp) REVERT: I 164 MET cc_start: 0.7159 (ptm) cc_final: 0.6221 (ppp) REVERT: I 166 ARG cc_start: 0.5987 (ptt-90) cc_final: 0.4375 (ttp80) REVERT: J 79 GLU cc_start: 0.5693 (tt0) cc_final: 0.4362 (pm20) REVERT: J 115 LYS cc_start: 0.6936 (mttt) cc_final: 0.6681 (ttpt) REVERT: J 122 ARG cc_start: 0.6828 (tpt170) cc_final: 0.6320 (mmt180) REVERT: J 127 ASP cc_start: 0.4751 (t0) cc_final: 0.3978 (p0) REVERT: J 170 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7105 (pp20) REVERT: K 109 TYR cc_start: 0.8792 (t80) cc_final: 0.8543 (t80) REVERT: M 111 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6670 (p0) REVERT: N 36 VAL cc_start: 0.4393 (OUTLIER) cc_final: 0.4166 (p) REVERT: O 120 MET cc_start: 0.7328 (mmm) cc_final: 0.7043 (mmt) REVERT: Q 99 MET cc_start: 0.8873 (mtm) cc_final: 0.8591 (mtp) REVERT: R 64 MET cc_start: 0.8572 (mmm) cc_final: 0.8346 (mmm) REVERT: U 46 MET cc_start: 0.8049 (mmm) cc_final: 0.7276 (mmt) REVERT: V 165 ILE cc_start: 0.3854 (OUTLIER) cc_final: 0.3423 (mt) REVERT: W 57 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: X 233 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6522 (tm-30) REVERT: Y 153 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8497 (tt) REVERT: Y 155 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8121 (mm) REVERT: e 224 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7481 (tm-30) REVERT: h 56 ARG cc_start: 0.5530 (ptt180) cc_final: 0.4932 (ttp80) REVERT: h 67 GLN cc_start: 0.7451 (pm20) cc_final: 0.6640 (tt0) REVERT: h 116 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6607 (mmt180) REVERT: k 11 ARG cc_start: 0.5075 (tpp-160) cc_final: 0.4790 (tpm170) REVERT: k 76 MET cc_start: 0.6319 (mtm) cc_final: 0.5755 (mtp) REVERT: k 92 SER cc_start: 0.6108 (p) cc_final: 0.5722 (m) REVERT: l 58 ASP cc_start: 0.1516 (OUTLIER) cc_final: 0.0884 (p0) REVERT: l 73 MET cc_start: 0.3777 (mmm) cc_final: 0.3196 (mmm) REVERT: l 113 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6858 (mp0) REVERT: l 127 TRP cc_start: 0.5802 (m-10) cc_final: 0.5594 (m-10) REVERT: l 134 LYS cc_start: 0.6257 (tttp) cc_final: 0.5839 (tptt) REVERT: m 51 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5524 (mm) REVERT: m 58 LYS cc_start: 0.6763 (mttt) cc_final: 0.6255 (mmtm) REVERT: q 127 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8373 (mtpp) REVERT: q 145 LYS cc_start: 0.7239 (mttp) cc_final: 0.6835 (mttp) REVERT: q 155 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7682 (ptt-90) REVERT: r 190 THR cc_start: 0.8232 (m) cc_final: 0.7785 (p) outliers start: 238 outliers final: 178 residues processed: 929 average time/residue: 0.9454 time to fit residues: 1532.8951 Evaluate side-chains 919 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 722 time to evaluate : 7.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 71 TYR Chi-restraints excluded: chain t residue 73 VAL Chi-restraints excluded: chain t residue 81 CYS Chi-restraints excluded: chain t residue 84 ASN Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 204 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain t residue 230 VAL Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 189 GLU Chi-restraints excluded: chain u residue 195 THR Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain x residue 100 ASN Chi-restraints excluded: chain x residue 163 LEU Chi-restraints excluded: chain x residue 233 VAL Chi-restraints excluded: chain y residue 96 MET Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 180 LEU Chi-restraints excluded: chain y residue 223 LEU Chi-restraints excluded: chain y residue 261 ILE Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 175 ILE Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 372 ASN Chi-restraints excluded: chain 5 residue 379 ASP Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 187 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 276 ASP Chi-restraints excluded: chain 6 residue 280 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 218 THR Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 112 ASP Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain 9 residue 127 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 80 ILE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 154 ILE Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 156 GLU Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 132 SER Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 94 HIS Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 165 ILE Chi-restraints excluded: chain V residue 169 THR Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 233 GLU Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 89 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 122 ASP Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain d residue 134 ILE Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 240 THR Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 65 ASN Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain l residue 58 ASP Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 82 ASP Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 74 ILE Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 78 THR Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 132 GLU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 116 GLU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 243 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 953 optimal weight: 5.9990 chunk 1004 optimal weight: 7.9990 chunk 916 optimal weight: 5.9990 chunk 977 optimal weight: 20.0000 chunk 588 optimal weight: 4.9990 chunk 425 optimal weight: 8.9990 chunk 767 optimal weight: 20.0000 chunk 299 optimal weight: 8.9990 chunk 883 optimal weight: 10.0000 chunk 924 optimal weight: 5.9990 chunk 973 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 299 HIS ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 354 GLN 7 207 HIS ** 7 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 HIS ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 HIS ** d 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 GLN ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 116061 Z= 0.374 Angle : 0.645 17.602 164252 Z= 0.323 Chirality : 0.041 0.239 19153 Planarity : 0.005 0.122 15513 Dihedral : 19.739 178.708 33510 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.65 % Allowed : 12.29 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.23 (0.09), residues: 9449 helix: 0.86 (0.09), residues: 3288 sheet: -0.38 (0.14), residues: 1319 loop : -0.07 (0.09), residues: 4842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 7 143 HIS 0.023 0.001 HIS t 299 PHE 0.023 0.002 PHE 5 60 TYR 0.029 0.002 TYR c 305 ARG 0.008 0.001 ARG M 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 738 time to evaluate : 7.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 229 MET cc_start: 0.4328 (ttm) cc_final: 0.3602 (ttm) REVERT: t 330 MET cc_start: 0.4240 (ppp) cc_final: 0.1979 (tpp) REVERT: t 361 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.5983 (m-30) REVERT: t 365 GLN cc_start: 0.3978 (OUTLIER) cc_final: 0.2817 (pt0) REVERT: u 126 ILE cc_start: 0.7956 (mp) cc_final: 0.7672 (mp) REVERT: u 180 MET cc_start: 0.6830 (ptp) cc_final: 0.6269 (mpp) REVERT: u 189 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: v 40 ARG cc_start: 0.7002 (mtm180) cc_final: 0.6170 (tpt170) REVERT: x 58 ASP cc_start: 0.6579 (t70) cc_final: 0.6149 (t0) REVERT: x 83 TRP cc_start: 0.6432 (p-90) cc_final: 0.5955 (p-90) REVERT: x 241 TRP cc_start: 0.6760 (m100) cc_final: 0.5724 (m100) REVERT: x 380 MET cc_start: 0.8151 (pmm) cc_final: 0.7865 (pmm) REVERT: y 96 MET cc_start: 0.4018 (OUTLIER) cc_final: 0.3594 (tmm) REVERT: y 247 ASP cc_start: 0.7309 (t0) cc_final: 0.7068 (t0) REVERT: y 291 LYS cc_start: 0.6318 (pttp) cc_final: 0.5700 (mtmm) REVERT: 0 170 GLN cc_start: 0.7595 (mt0) cc_final: 0.7188 (mm110) REVERT: 7 81 MET cc_start: 0.8106 (mmm) cc_final: 0.7445 (mmt) REVERT: 7 142 TYR cc_start: 0.7253 (t80) cc_final: 0.6870 (t80) REVERT: 7 323 MET cc_start: 0.6595 (mmm) cc_final: 0.5558 (mmt) REVERT: 9 102 LYS cc_start: 0.7557 (tttt) cc_final: 0.7268 (mptt) REVERT: 9 105 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7383 (ttpp) REVERT: D 165 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7838 (m-40) REVERT: D 292 MET cc_start: 0.7985 (mmm) cc_final: 0.7777 (mmp) REVERT: E 77 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.6844 (tt) REVERT: H 100 GLN cc_start: 0.6762 (mp10) cc_final: 0.5997 (mp-120) REVERT: H 145 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7383 (pp) REVERT: I 164 MET cc_start: 0.7131 (ptm) cc_final: 0.6186 (ppp) REVERT: I 166 ARG cc_start: 0.6113 (ptt-90) cc_final: 0.4896 (mtt90) REVERT: J 79 GLU cc_start: 0.5945 (tt0) cc_final: 0.4413 (pm20) REVERT: J 115 LYS cc_start: 0.6853 (mttt) cc_final: 0.6626 (ttpt) REVERT: J 127 ASP cc_start: 0.4790 (t0) cc_final: 0.3973 (p0) REVERT: L 91 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7029 (ttt) REVERT: L 142 GLN cc_start: 0.7127 (mt0) cc_final: 0.6391 (mt0) REVERT: M 111 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6696 (p0) REVERT: Q 99 MET cc_start: 0.8813 (mtm) cc_final: 0.8288 (mtm) REVERT: R 64 MET cc_start: 0.8562 (mmm) cc_final: 0.8344 (mmm) REVERT: V 165 ILE cc_start: 0.4032 (OUTLIER) cc_final: 0.3394 (mm) REVERT: W 57 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: X 233 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6590 (tm-30) REVERT: Y 153 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8528 (tt) REVERT: Y 155 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8111 (mm) REVERT: Y 206 ASP cc_start: 0.7584 (p0) cc_final: 0.7300 (p0) REVERT: d 233 TYR cc_start: 0.6692 (t80) cc_final: 0.6296 (t80) REVERT: e 224 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7422 (tm-30) REVERT: h 56 ARG cc_start: 0.5562 (ptt180) cc_final: 0.4927 (ttp80) REVERT: h 97 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7367 (mmmt) REVERT: h 116 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6620 (mmt180) REVERT: k 11 ARG cc_start: 0.5145 (tpp-160) cc_final: 0.4718 (tpm170) REVERT: k 76 MET cc_start: 0.6356 (mtm) cc_final: 0.5776 (mtp) REVERT: k 92 SER cc_start: 0.6177 (p) cc_final: 0.5823 (m) REVERT: l 73 MET cc_start: 0.3895 (mmm) cc_final: 0.3545 (mmm) REVERT: l 99 MET cc_start: 0.1763 (mmt) cc_final: 0.1096 (mmt) REVERT: l 113 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6772 (mp0) REVERT: l 127 TRP cc_start: 0.5902 (m-10) cc_final: 0.5591 (m100) REVERT: l 134 LYS cc_start: 0.6300 (tttp) cc_final: 0.5885 (tptt) REVERT: m 58 LYS cc_start: 0.6840 (mttt) cc_final: 0.6235 (mmtm) REVERT: p 53 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7663 (mm-40) REVERT: p 136 THR cc_start: 0.7521 (m) cc_final: 0.6918 (t) REVERT: q 127 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8358 (mtpp) REVERT: q 142 ASN cc_start: 0.8491 (m-40) cc_final: 0.8111 (p0) REVERT: q 155 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7725 (ptt-90) REVERT: r 190 THR cc_start: 0.8202 (m) cc_final: 0.7730 (p) outliers start: 223 outliers final: 188 residues processed: 898 average time/residue: 0.9294 time to fit residues: 1465.4163 Evaluate side-chains 920 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 717 time to evaluate : 7.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 71 TYR Chi-restraints excluded: chain t residue 84 ASN Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 204 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain t residue 230 VAL Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 299 HIS Chi-restraints excluded: chain t residue 361 ASP Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 189 GLU Chi-restraints excluded: chain u residue 195 THR Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain x residue 163 LEU Chi-restraints excluded: chain x residue 233 VAL Chi-restraints excluded: chain y residue 96 MET Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 180 LEU Chi-restraints excluded: chain y residue 208 THR Chi-restraints excluded: chain y residue 223 LEU Chi-restraints excluded: chain y residue 251 SER Chi-restraints excluded: chain y residue 261 ILE Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 157 VAL Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 175 ILE Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 3 residue 188 VAL Chi-restraints excluded: chain 4 residue 71 VAL Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 372 ASN Chi-restraints excluded: chain 5 residue 379 ASP Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 187 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 243 ASN Chi-restraints excluded: chain 6 residue 276 ASP Chi-restraints excluded: chain 6 residue 280 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 218 THR Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 8 residue 177 HIS Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 112 ASP Chi-restraints excluded: chain 9 residue 120 GLU Chi-restraints excluded: chain 9 residue 127 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 80 ILE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 89 HIS Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 167 CYS Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 166 SER Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain T residue 132 SER Chi-restraints excluded: chain T residue 184 LYS Chi-restraints excluded: chain T residue 201 THR Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 94 HIS Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 165 ILE Chi-restraints excluded: chain V residue 169 THR Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 233 GLU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 89 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain d residue 134 ILE Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 240 THR Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 90 SER Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 65 ASN Chi-restraints excluded: chain j residue 72 THR Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain l residue 58 ASP Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 74 ILE Chi-restraints excluded: chain o residue 88 ILE Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 78 THR Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 132 GLU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 86 VAL Chi-restraints excluded: chain r residue 116 GLU Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 183 ASP Chi-restraints excluded: chain s residue 97 THR Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 178 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 404 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 641 optimal weight: 2.9990 chunk 1033 optimal weight: 3.9990 chunk 630 optimal weight: 0.7980 chunk 490 optimal weight: 5.9990 chunk 718 optimal weight: 4.9990 chunk 1083 optimal weight: 1.9990 chunk 997 optimal weight: 8.9990 chunk 863 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 666 optimal weight: 0.3980 chunk 529 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 198 ASN t 299 HIS t 314 GLN ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 384 GLN 6 249 GLN 7 207 HIS ** 7 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN H 126 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS Q 139 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN Z 67 HIS b 123 ASN ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 93 ASN g 121 GLN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.101 116061 Z= 0.141 Angle : 0.542 17.909 164252 Z= 0.271 Chirality : 0.036 0.235 19153 Planarity : 0.004 0.113 15513 Dihedral : 19.651 179.177 33510 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.73 % Allowed : 13.38 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.64 (0.09), residues: 9449 helix: 1.24 (0.09), residues: 3289 sheet: -0.21 (0.14), residues: 1332 loop : 0.16 (0.09), residues: 4828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP 7 143 HIS 0.013 0.001 HIS d 193 PHE 0.024 0.001 PHE y 301 TYR 0.029 0.001 TYR 8 124 ARG 0.009 0.000 ARG t 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 787 time to evaluate : 7.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 229 MET cc_start: 0.4244 (ttm) cc_final: 0.3921 (ttm) REVERT: t 330 MET cc_start: 0.4172 (ppp) cc_final: 0.1921 (tpp) REVERT: t 365 GLN cc_start: 0.3739 (OUTLIER) cc_final: 0.2783 (pt0) REVERT: u 126 ILE cc_start: 0.7857 (mp) cc_final: 0.7652 (mp) REVERT: u 171 ASP cc_start: 0.7468 (t0) cc_final: 0.6912 (t0) REVERT: u 189 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: v 40 ARG cc_start: 0.6991 (mtm180) cc_final: 0.6168 (tpt170) REVERT: x 58 ASP cc_start: 0.6624 (t70) cc_final: 0.6210 (t0) REVERT: x 83 TRP cc_start: 0.6370 (p-90) cc_final: 0.5886 (p-90) REVERT: x 241 TRP cc_start: 0.6838 (m100) cc_final: 0.5798 (m100) REVERT: x 380 MET cc_start: 0.8054 (pmm) cc_final: 0.7767 (pmm) REVERT: y 247 ASP cc_start: 0.7265 (t0) cc_final: 0.7037 (t0) REVERT: y 291 LYS cc_start: 0.6281 (pttp) cc_final: 0.5630 (mtmm) REVERT: 0 170 GLN cc_start: 0.7465 (mt0) cc_final: 0.7098 (mm110) REVERT: 7 81 MET cc_start: 0.7933 (mmm) cc_final: 0.7463 (mmt) REVERT: 7 142 TYR cc_start: 0.7137 (t80) cc_final: 0.6871 (t80) REVERT: 7 323 MET cc_start: 0.6532 (mmm) cc_final: 0.5702 (mmt) REVERT: 9 102 LYS cc_start: 0.7377 (tttt) cc_final: 0.7054 (mptt) REVERT: 9 105 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7376 (ttpp) REVERT: D 275 TRP cc_start: 0.7689 (t60) cc_final: 0.7451 (t60) REVERT: D 295 TYR cc_start: 0.5179 (m-10) cc_final: 0.4579 (m-80) REVERT: E 77 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.6916 (tt) REVERT: H 100 GLN cc_start: 0.6562 (mp10) cc_final: 0.6206 (mp-120) REVERT: H 145 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7409 (pp) REVERT: I 164 MET cc_start: 0.7213 (ptm) cc_final: 0.6250 (ppp) REVERT: I 166 ARG cc_start: 0.5869 (ptt-90) cc_final: 0.4760 (mtt90) REVERT: J 79 GLU cc_start: 0.5741 (tt0) cc_final: 0.4332 (pm20) REVERT: J 115 LYS cc_start: 0.6752 (mttt) cc_final: 0.6523 (ttpt) REVERT: J 127 ASP cc_start: 0.4276 (t0) cc_final: 0.3649 (p0) REVERT: K 109 TYR cc_start: 0.8647 (t80) cc_final: 0.8446 (t80) REVERT: K 121 MET cc_start: 0.8296 (mtt) cc_final: 0.8044 (mtt) REVERT: N 118 MET cc_start: 0.7407 (mtt) cc_final: 0.6924 (mtm) REVERT: R 64 MET cc_start: 0.8399 (mmm) cc_final: 0.8167 (mmm) REVERT: U 46 MET cc_start: 0.7901 (mmm) cc_final: 0.7013 (mmm) REVERT: V 66 GLU cc_start: 0.7304 (pm20) cc_final: 0.7007 (pm20) REVERT: V 165 ILE cc_start: 0.3912 (OUTLIER) cc_final: 0.3292 (mm) REVERT: W 57 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: X 233 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: Y 153 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8415 (tt) REVERT: Y 155 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7962 (mm) REVERT: d 187 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6970 (pp20) REVERT: d 248 PHE cc_start: 0.6597 (m-80) cc_final: 0.6096 (m-80) REVERT: e 224 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7495 (tm-30) REVERT: h 56 ARG cc_start: 0.5377 (ptt180) cc_final: 0.4878 (ttp80) REVERT: h 95 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7420 (mmp80) REVERT: h 116 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6491 (mmt180) REVERT: j 100 GLU cc_start: 0.7627 (pp20) cc_final: 0.7080 (pp20) REVERT: k 11 ARG cc_start: 0.5012 (tpp-160) cc_final: 0.4565 (tpm170) REVERT: k 76 MET cc_start: 0.6571 (mtm) cc_final: 0.6209 (mtp) REVERT: k 92 SER cc_start: 0.6453 (p) cc_final: 0.6105 (m) REVERT: l 58 ASP cc_start: 0.1635 (OUTLIER) cc_final: 0.1162 (p0) REVERT: l 73 MET cc_start: 0.4163 (mmm) cc_final: 0.3404 (mmm) REVERT: l 99 MET cc_start: 0.1394 (mmt) cc_final: 0.0918 (mmt) REVERT: l 113 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6845 (mp0) REVERT: l 127 TRP cc_start: 0.5944 (m-10) cc_final: 0.5683 (m100) REVERT: l 134 LYS cc_start: 0.6169 (tttp) cc_final: 0.5650 (mtpp) REVERT: m 58 LYS cc_start: 0.6778 (mttt) cc_final: 0.6293 (mmtm) REVERT: p 136 THR cc_start: 0.7242 (m) cc_final: 0.6954 (p) REVERT: q 142 ASN cc_start: 0.8469 (m-40) cc_final: 0.8156 (p0) REVERT: q 155 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7750 (ptt-90) REVERT: r 190 THR cc_start: 0.8176 (m) cc_final: 0.7716 (p) outliers start: 146 outliers final: 114 residues processed: 886 average time/residue: 1.0051 time to fit residues: 1559.6272 Evaluate side-chains 858 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 732 time to evaluate : 7.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 71 TYR Chi-restraints excluded: chain t residue 84 ASN Chi-restraints excluded: chain t residue 131 ARG Chi-restraints excluded: chain t residue 204 VAL Chi-restraints excluded: chain t residue 205 THR Chi-restraints excluded: chain t residue 241 LEU Chi-restraints excluded: chain t residue 265 ILE Chi-restraints excluded: chain t residue 299 HIS Chi-restraints excluded: chain t residue 365 GLN Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 189 GLU Chi-restraints excluded: chain u residue 195 THR Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain x residue 163 LEU Chi-restraints excluded: chain x residue 233 VAL Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 180 LEU Chi-restraints excluded: chain y residue 223 LEU Chi-restraints excluded: chain 0 residue 154 ILE Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 175 ILE Chi-restraints excluded: chain 1 residue 26 THR Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 182 ASP Chi-restraints excluded: chain 4 residue 93 LYS Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 6 residue 88 ILE Chi-restraints excluded: chain 6 residue 187 VAL Chi-restraints excluded: chain 6 residue 205 THR Chi-restraints excluded: chain 6 residue 276 ASP Chi-restraints excluded: chain 6 residue 280 ASP Chi-restraints excluded: chain 7 residue 56 LEU Chi-restraints excluded: chain 7 residue 93 MET Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 143 TRP Chi-restraints excluded: chain 7 residue 184 VAL Chi-restraints excluded: chain 7 residue 263 VAL Chi-restraints excluded: chain 9 residue 45 THR Chi-restraints excluded: chain 9 residue 127 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain P residue 97 GLN Chi-restraints excluded: chain P residue 161 LEU Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 246 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 200 ILE Chi-restraints excluded: chain U residue 109 ASP Chi-restraints excluded: chain V residue 86 VAL Chi-restraints excluded: chain V residue 94 HIS Chi-restraints excluded: chain V residue 122 LEU Chi-restraints excluded: chain V residue 165 ILE Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 117 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 233 GLU Chi-restraints excluded: chain Y residue 114 THR Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 136 ASN Chi-restraints excluded: chain a residue 119 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 89 ILE Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 220 ILE Chi-restraints excluded: chain c residue 231 MET Chi-restraints excluded: chain d residue 134 ILE Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 64 THR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 240 THR Chi-restraints excluded: chain f residue 173 ILE Chi-restraints excluded: chain g residue 43 ASP Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 90 SER Chi-restraints excluded: chain h residue 116 ARG Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain k residue 54 ASP Chi-restraints excluded: chain l residue 58 ASP Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain p residue 46 ASP Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain p residue 132 GLU Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 116 GLU Chi-restraints excluded: chain s residue 152 GLN Chi-restraints excluded: chain s residue 243 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 685 optimal weight: 6.9990 chunk 919 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 chunk 795 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 239 optimal weight: 20.0000 chunk 864 optimal weight: 20.0000 chunk 361 optimal weight: 10.0000 chunk 887 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 345 ASN ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 207 HIS ** 7 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN Z 67 HIS b 123 ASN ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 GLN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 91 GLN ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 184 ASN ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.099133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.078141 restraints weight = 362112.242| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.21 r_work: 0.3367 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.317 116061 Z= 0.249 Angle : 0.589 59.154 164252 Z= 0.307 Chirality : 0.039 1.260 19153 Planarity : 0.004 0.198 15513 Dihedral : 19.647 179.168 33510 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 1.55 % Allowed : 13.57 % Favored : 84.88 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.63 (0.09), residues: 9449 helix: 1.23 (0.09), residues: 3290 sheet: -0.21 (0.14), residues: 1345 loop : 0.16 (0.09), residues: 4814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP 7 143 HIS 0.272 0.001 HIS t 299 PHE 0.022 0.001 PHE y 301 TYR 0.024 0.001 TYR 8 124 ARG 0.012 0.000 ARG D 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29004.21 seconds wall clock time: 506 minutes 30.45 seconds (30390.45 seconds total)