Starting phenix.real_space_refine on Fri Dec 8 02:06:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ods_12846/12_2023/7ods_12846_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ods_12846/12_2023/7ods_12846.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ods_12846/12_2023/7ods_12846_neut_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/7ods_12846/12_2023/7ods_12846_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ods_12846/12_2023/7ods_12846_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ods_12846/12_2023/7ods_12846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ods_12846/12_2023/7ods_12846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ods_12846/12_2023/7ods_12846_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ods_12846/12_2023/7ods_12846_neut_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= -0.002 sd= 0.190 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 8 8.98 5 Fe 2 7.16 5 Zn 2 6.06 5 P 1519 5.49 5 Mg 88 5.21 5 S 334 5.16 5 C 62907 2.51 5 N 19536 2.21 5 O 23943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 108339 Number of models: 1 Model: "" Number of chains: 67 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: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2660 Classifications: {'peptide': 336} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 319} 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: "z" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1366 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 36 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: 30407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1445, 30407 Classifications: {'RNA': 1445} Modifications used: {'rna2p_pur': 148, 'rna2p_pyr': 109, 'rna3p': 31, 'rna3p_pur': 601, 'rna3p_pyr': 556} Link IDs: {'rna2p': 257, 'rna3p': 1187} Chain breaks: 11 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 30 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: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1331 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 15, 'TRANS': 148} 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: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1702 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 191} Chain breaks: 1 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: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1653 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 183} 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: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1824 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 15, 'TRANS': 207} 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: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 688 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 105 Unusual residues: {' K': 8, ' MG': 85} Classifications: {'RNA': 1, 'undetermined': 93} Modifications used: {'rna3p': 1} Link IDs: {None: 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" 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 8415 SG CYS 0 110 68.709 101.997 171.458 1.00 66.12 S ATOM 8437 SG CYS 0 113 67.420 99.692 168.641 1.00 66.60 S ATOM 8517 SG CYS 0 123 69.440 102.736 167.762 1.00 54.69 S ATOM 8540 SG CYS 0 126 65.923 103.110 169.268 1.00 66.02 S ATOM 10807 SG CYS 4 76 169.159 156.158 165.328 1.00 91.56 S ATOM 10830 SG CYS 4 79 167.252 152.862 165.269 1.00 84.34 S ATOM 10954 SG CYS 4 92 166.043 155.727 167.486 1.00 75.97 S ATOM 60760 SG CYS I 64 184.728 118.101 171.591 1.00 91.70 S ATOM A032N SG CYS r 73 185.433 118.279 175.254 1.00 75.27 S ATOM A0322 SG CYS r 70 183.446 121.569 176.538 1.00 77.77 S ATOM A03AT SG CYS r 108 182.026 123.248 173.429 1.00 71.12 S Time building chain proxies: 41.41, per 1000 atoms: 0.38 Number of scatterers: 108339 At special positions: 0 Unit cell: (259.793, 246.749, 235.879, 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 8 19.00 S 334 16.00 P 1519 15.00 Mg 88 11.99 O 23943 8.00 N 19536 7.00 C 62907 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.65 Conformation dependent library (CDL) restraints added in 10.9 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 r 73 " pdb="FE1 FES r 201 " - pdb=" SG CYS I 64 " 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 0 113 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 110 " pdb=" ZN 4 201 " pdb="ZN ZN 4 201 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 92 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 79 " Number of angles added : 9 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17686 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: 319 helices and 80 sheets defined 43.3% alpha, 13.6% beta 305 base pairs and 802 stacking pairs defined. Time for finding SS restraints: 65.17 Creating SS restraints... Processing helix chain 'u' and resid 93 through 105 Processing helix chain 'u' and resid 131 through 149 Processing helix chain 'u' and resid 181 through 189 removed outlier: 3.650A 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: 3.864A pdb=" N VAL v 9 " --> pdb=" O SER v 5 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU v 12 " --> pdb=" O ALA v 8 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR v 13 " --> pdb=" O VAL v 9 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG v 24 " --> pdb=" O GLY v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 45 removed outlier: 3.557A pdb=" N LYS v 41 " --> pdb=" O ARG v 37 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN v 42 " --> pdb=" O GLU v 38 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS v 44 " --> pdb=" O ARG v 40 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU v 45 " --> pdb=" O LYS v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 47 through 64 removed outlier: 3.911A pdb=" N GLN v 54 " --> pdb=" O ALA v 50 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL v 60 " --> pdb=" O GLU v 56 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.543A pdb=" N ILE w 79 " --> pdb=" O THR w 75 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 5.089A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.170A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU w 138 " --> pdb=" O ASP w 134 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N MET w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 removed outlier: 3.692A pdb=" N ASP w 150 " --> pdb=" O ASP w 146 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS w 152 " --> pdb=" O ILE w 148 " (cutoff:3.500A) Processing helix chain 'w' and resid 103 through 109 Processing helix chain 'x' and resid 39 through 57 removed outlier: 4.108A pdb=" N VAL x 54 " --> pdb=" O MET x 50 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN x 55 " --> pdb=" O THR x 51 " (cutoff:3.500A) Processing helix chain 'x' and resid 58 through 70 removed outlier: 4.576A pdb=" N SER x 62 " --> pdb=" O ASP x 58 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER x 66 " --> pdb=" O SER x 62 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU x 70 " --> pdb=" O SER x 66 " (cutoff:3.500A) Processing helix chain 'x' and resid 82 through 94 Processing helix chain 'x' and resid 97 through 109 removed outlier: 3.632A pdb=" N TRP x 106 " --> pdb=" O ALA x 102 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU x 107 " --> pdb=" O ILE x 103 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU x 108 " --> pdb=" O SER x 104 " (cutoff:3.500A) Processing helix chain 'x' and resid 159 through 170 removed outlier: 3.945A pdb=" N LEU x 163 " --> pdb=" O ASP x 159 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU x 164 " --> pdb=" O ALA x 160 " (cutoff:3.500A) Proline residue: x 165 - end of helix removed outlier: 3.947A pdb=" N GLY x 170 " --> pdb=" O VAL x 166 " (cutoff:3.500A) Processing helix chain 'x' and resid 185 through 195 removed outlier: 4.154A pdb=" N ALA x 190 " --> pdb=" O GLY x 186 " (cutoff:3.500A) removed outlier: 3.720A 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 229 removed outlier: 3.608A pdb=" N ARG x 226 " --> pdb=" O PRO x 222 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY x 228 " --> pdb=" O GLU x 224 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASN x 229 " --> pdb=" O ILE x 225 " (cutoff:3.500A) Processing helix chain 'x' and resid 237 through 245 removed outlier: 4.301A pdb=" N TRP x 241 " --> pdb=" O ASP x 237 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY x 242 " --> pdb=" O GLY x 238 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU x 243 " --> pdb=" O ARG x 239 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU x 245 " --> pdb=" O TRP x 241 " (cutoff:3.500A) Processing helix chain 'x' and resid 260 through 267 removed outlier: 3.717A pdb=" N HIS x 266 " --> pdb=" O ARG x 262 " (cutoff:3.500A) Processing helix chain 'x' and resid 274 through 300 removed outlier: 4.881A pdb=" N LYS x 279 " --> pdb=" O ARG x 275 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU x 280 " --> pdb=" O SER x 276 " (cutoff:3.500A) Proline residue: x 285 - end of helix removed outlier: 5.919A pdb=" N LYS x 300 " --> pdb=" O LEU x 296 " (cutoff:3.500A) Processing helix chain 'x' and resid 313 through 331 removed outlier: 4.752A pdb=" N TYR x 319 " --> pdb=" O LEU x 315 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL x 320 " --> pdb=" O GLN x 316 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL x 321 " --> pdb=" O ASN x 317 " (cutoff:3.500A) Processing helix chain 'x' and resid 341 through 349 removed outlier: 3.652A pdb=" N VAL x 347 " --> pdb=" O HIS x 343 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE x 348 " --> pdb=" O PHE x 344 " (cutoff:3.500A) Processing helix chain 'y' and resid 88 through 103 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 Processing helix chain 'y' and resid 173 through 183 removed outlier: 6.229A pdb=" N LYS y 177 " --> pdb=" O GLU y 173 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG y 178 " --> pdb=" O GLY y 174 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL y 179 " --> pdb=" O LYS y 175 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR y 181 " --> pdb=" O LYS y 177 " (cutoff:3.500A) Processing helix chain 'y' and resid 190 through 203 removed outlier: 3.680A 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: 4.461A pdb=" N ARG y 224 " --> pdb=" O PRO y 220 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASP y 226 " --> pdb=" O VAL y 222 " (cutoff:3.500A) Processing helix chain 'y' and resid 227 through 239 removed outlier: 3.558A 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 removed outlier: 3.576A pdb=" N TYR y 267 " --> pdb=" O GLN y 263 " (cutoff:3.500A) Processing helix chain 'y' and resid 289 through 295 Processing helix chain 'y' and resid 297 through 305 removed outlier: 3.754A pdb=" N ALA y 303 " --> pdb=" O ALA y 299 " (cutoff:3.500A) Processing helix chain 'y' and resid 309 through 331 removed outlier: 3.677A pdb=" N PHE y 313 " --> pdb=" O SER y 309 " (cutoff:3.500A) Processing helix chain 'z' and resid 4 through 17 removed outlier: 4.852A pdb=" N PHE z 8 " --> pdb=" O CYS z 4 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS z 9 " --> pdb=" O ARG z 5 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU z 10 " --> pdb=" O SER z 6 " (cutoff:3.500A) Processing helix chain 'z' and resid 34 through 45 Processing helix chain 'z' and resid 82 through 94 removed outlier: 3.547A pdb=" N SER z 86 " --> pdb=" O ASP z 82 " (cutoff:3.500A) Proline residue: z 94 - end of helix Processing helix chain 'z' and resid 112 through 135 removed outlier: 3.864A pdb=" N ASP z 118 " --> pdb=" O ASP z 114 " (cutoff:3.500A) Proline residue: z 132 - end of helix Processing helix chain 'z' and resid 148 through 162 removed outlier: 4.568A pdb=" N ARG z 152 " --> pdb=" O GLY z 148 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG z 153 " --> pdb=" O SER z 149 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 96 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: 4.372A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 73 through 86 Processing helix chain '3' and resid 107 through 114 removed outlier: 3.955A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 4.084A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.737A 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: 3.526A pdb=" N ARG 3 143 " --> pdb=" O ALA 3 139 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE 3 147 " --> pdb=" O ARG 3 143 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 5.131A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 5.221A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 52 removed outlier: 4.536A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 47 through 52' Processing helix chain '5' and resid 116 through 125 removed outlier: 3.861A pdb=" N TRP 5 122 " --> pdb=" O LYS 5 118 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 142 removed outlier: 3.746A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 4.395A 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 Proline residue: 5 178 - end of helix removed outlier: 3.549A pdb=" N VAL 5 181 " --> pdb=" O CYS 5 177 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU 5 184 " --> pdb=" O ILE 5 180 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER 5 190 " --> pdb=" O GLN 5 186 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.599A 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: 3.754A pdb=" N THR 5 248 " --> pdb=" O GLU 5 244 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.322A pdb=" N LEU 5 304 " --> pdb=" O ARG 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 removed outlier: 3.670A pdb=" N ARG 5 310 " --> pdb=" O PRO 5 306 " (cutoff:3.500A) Processing helix chain '5' and resid 407 through 420 removed outlier: 4.345A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 3.641A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.932A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 116 Processing helix chain '6' and resid 117 through 126 Processing helix chain '6' and resid 131 through 143 removed outlier: 3.750A pdb=" N ARG 6 141 " --> pdb=" O ALA 6 137 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 156 removed outlier: 3.577A 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: 3.818A pdb=" N GLY 6 248 " --> pdb=" O ARG 6 244 " (cutoff:3.500A) removed outlier: 5.578A 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: 3.542A pdb=" N LYS 6 306 " --> pdb=" O ASP 6 302 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 removed outlier: 4.079A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE 6 330 " --> pdb=" O SER 6 326 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 371 removed outlier: 3.735A pdb=" N ARG 6 368 " --> pdb=" O ARG 6 364 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG 6 370 " --> pdb=" O LEU 6 366 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 364 through 371' Processing helix chain '6' and resid 157 through 163 removed outlier: 4.081A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 removed outlier: 4.137A pdb=" N THR 7 41 " --> pdb=" O PRO 7 37 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU 7 42 " --> pdb=" O THR 7 38 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG 7 44 " --> pdb=" O LEU 7 40 " (cutoff:3.500A) removed outlier: 3.518A 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: 3.614A 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: 3.501A pdb=" N VAL 7 153 " --> pdb=" O MET 7 149 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU 7 155 " --> pdb=" O GLY 7 151 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG 7 156 " --> pdb=" O CYS 7 152 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 191 removed outlier: 3.966A pdb=" N ASP 7 190 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 5.559A 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: 3.740A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 222 through 231 Processing helix chain '7' and resid 233 through 248 removed outlier: 3.712A pdb=" N VAL 7 237 " --> pdb=" O SER 7 233 " (cutoff:3.500A) removed outlier: 3.696A 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: 3.645A pdb=" N LYS 7 315 " --> pdb=" O THR 7 311 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N MET 7 323 " --> pdb=" O ARG 7 319 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 3.705A pdb=" N CYS 7 275 " --> pdb=" O THR 7 272 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 107 through 154 removed outlier: 3.708A pdb=" N LEU 8 123 " --> pdb=" O LYS 8 119 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN 8 126 " --> pdb=" O SER 8 122 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 8 152 " --> pdb=" O GLU 8 148 " (cutoff:3.500A) Processing helix chain '8' and resid 155 through 164 removed outlier: 3.808A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '9' and resid 27 through 35 removed outlier: 5.592A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.584A 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 95 Processing helix chain '9' and resid 96 through 107 Processing helix chain '9' and resid 110 through 118 removed outlier: 4.039A pdb=" N LEU 9 114 " --> pdb=" O ASP 9 110 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU 9 115 " --> pdb=" O PRO 9 111 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LYS 9 116 " --> pdb=" O ASP 9 112 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR 9 117 " --> pdb=" O ASN 9 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.817A pdb=" N LEU D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix No H-bonds generated for 'chain 'D' and resid 183 through 188' Processing helix chain 'D' and resid 259 through 267 removed outlier: 4.079A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.486A pdb=" N ARG D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS D 285 " --> pdb=" O TRP D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.330A pdb=" N SER D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.927A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.875A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.586A pdb=" N ASN E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.582A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 158' Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.827A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.281A 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 92 through 108 removed outlier: 4.526A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 removed outlier: 3.939A pdb=" N LEU F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.724A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 4.301A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 5.013A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.125A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 89 Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.864A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.587A 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 115 through 121 removed outlier: 3.506A pdb=" N ARG H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 127 Processing helix chain 'H' and resid 133 through 149 Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.873A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 66 removed outlier: 3.514A pdb=" N LEU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) Proline residue: I 66 - end of helix No H-bonds generated for 'chain 'I' and resid 61 through 66' Processing helix chain 'I' and resid 76 through 92 removed outlier: 3.659A pdb=" N ARG I 84 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.720A 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: 3.657A pdb=" N ASP I 137 " --> pdb=" O PRO I 133 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.963A pdb=" N PHE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 5.225A 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: 3.653A pdb=" N ARG I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.406A 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: 3.652A 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: 3.540A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 3.766A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 134 removed outlier: 3.526A pdb=" N GLN J 133 " --> pdb=" O ALA J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 152 removed outlier: 3.772A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU J 151 " --> pdb=" O SER J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 192 removed outlier: 3.594A pdb=" N ALA J 165 " --> pdb=" O SER J 161 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE J 173 " --> pdb=" O LYS J 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 removed outlier: 3.646A pdb=" N ILE K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.742A 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 113 removed outlier: 3.502A pdb=" N MET K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.651A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.791A pdb=" N ASN K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 3.832A 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: 4.241A 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: 5.153A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 142 removed outlier: 4.087A pdb=" N ILE L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 20 removed outlier: 3.860A pdb=" N LEU M 13 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU M 16 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG M 17 " --> pdb=" O LEU M 13 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 4.027A 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: 3.592A pdb=" N ARG M 59 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.682A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (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: 3.828A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 removed outlier: 3.590A pdb=" N ASP M 185 " --> pdb=" O PRO M 181 " (cutoff:3.500A) removed outlier: 3.739A 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: 3.808A pdb=" N ARG M 196 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 4.399A 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: 3.654A pdb=" N ASP M 216 " --> pdb=" O PRO M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 241 removed outlier: 3.854A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix removed outlier: 3.553A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 251 removed outlier: 4.195A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.438A 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 removed outlier: 3.657A pdb=" N THR M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.606A pdb=" N SER M 296 " --> pdb=" O LYS M 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 74 removed outlier: 4.700A pdb=" N ARG N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 5.315A 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: 3.832A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS N 182 " --> pdb=" O GLN N 178 " (cutoff:3.500A) removed outlier: 3.552A 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: 5.088A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.473A 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: 4.012A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) removed outlier: 4.139A 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: 4.326A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.750A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.251A 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: 4.651A pdb=" N LEU P 56 " --> pdb=" O ASN P 52 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU P 57 " --> pdb=" O PRO P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 117 removed outlier: 4.690A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 5.475A 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: 5.511A 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: 4.148A 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 107 removed outlier: 3.764A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 194 removed outlier: 4.725A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 4.021A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.651A pdb=" N GLN Q 258 " --> pdb=" O MET Q 254 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.175A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 292 removed outlier: 3.514A pdb=" N ALA Q 280 " --> pdb=" O SER Q 276 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA Q 281 " --> pdb=" O LYS Q 277 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS Q 284 " --> pdb=" O ALA Q 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.545A pdb=" N GLU R 23 " --> pdb=" O PHE R 19 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 38 removed outlier: 4.843A pdb=" N ARG R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 80 removed outlier: 3.983A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.547A pdb=" N ASN R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 91 " --> pdb=" O ILE R 87 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 109 Processing helix chain 'R' and resid 110 through 134 removed outlier: 4.852A pdb=" N ASP R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 90 removed outlier: 3.948A pdb=" N ARG S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL S 88 " --> pdb=" O ASN S 84 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY S 90 " --> pdb=" O MET S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.655A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.353A 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: 4.082A pdb=" N LYS T 47 " --> pdb=" O ARG T 43 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN T 49 " --> pdb=" O TRP T 45 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS T 50 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE T 51 " --> pdb=" O LYS T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 89 removed outlier: 3.832A pdb=" N TYR T 83 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU T 84 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE T 88 " --> pdb=" O LEU T 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG T 89 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 103 removed outlier: 3.734A pdb=" N PHE T 102 " --> pdb=" O ALA T 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN T 103 " --> pdb=" O GLN T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 125 removed outlier: 4.334A pdb=" N LYS T 109 " --> pdb=" O LYS T 105 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 200 removed outlier: 3.754A 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: 5.264A 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: 5.697A pdb=" N TYR V 55 " --> pdb=" O ASP V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 121 removed outlier: 3.673A pdb=" N VAL V 120 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 116 through 121' Processing helix chain 'V' and resid 178 through 184 removed outlier: 3.613A 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: 4.082A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.705A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU X 16 " --> pdb=" O LYS X 12 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 35 removed outlier: 3.657A pdb=" N SER X 31 " --> pdb=" O HIS X 27 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU X 32 " --> pdb=" O TYR X 28 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 4.186A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.780A 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 removed outlier: 3.629A pdb=" N CYS X 154 " --> pdb=" O LYS X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 192 removed outlier: 3.563A pdb=" N TYR X 191 " --> pdb=" O ILE X 187 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS X 192 " --> pdb=" O TYR X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 204 removed outlier: 4.750A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 4.443A 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 Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.904A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.214A 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 86 through 94 removed outlier: 3.651A pdb=" N ARG Y 91 " --> pdb=" O CYS Y 87 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.922A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.330A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.818A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 3.813A pdb=" N LYS Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) removed outlier: 5.328A 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: 4.465A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS Y 236 " --> pdb=" O LYS Y 232 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS Y 237 " --> pdb=" O ILE Y 233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE Y 238 " --> pdb=" O LEU Y 234 " (cutoff:3.500A) Proline residue: Y 239 - end of helix Processing helix chain 'Z' and resid 42 through 47 removed outlier: 4.479A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 47' Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.628A pdb=" N HIS Z 53 " --> pdb=" O SER Z 49 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU Z 54 " --> pdb=" O PRO Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 114 removed outlier: 3.569A pdb=" N LYS Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL Z 112 " --> pdb=" O ALA Z 108 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 135 removed outlier: 5.334A pdb=" N SER Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 119 through 124 removed outlier: 4.694A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 4.007A 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 removed outlier: 3.686A pdb=" N LYS a 134 " --> pdb=" O HIS a 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.854A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 7.028A 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: 3.828A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG b 49 " --> pdb=" O GLU b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 59 removed outlier: 3.677A pdb=" N ARG b 56 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG b 57 " --> pdb=" O ASP b 53 " (cutoff:3.500A) Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 108 removed outlier: 6.028A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 137 removed outlier: 4.767A pdb=" N ASN b 135 " --> pdb=" O HIS b 131 " (cutoff:3.500A) removed outlier: 4.755A 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: 5.294A 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: 3.620A 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: 3.969A pdb=" N GLY c 76 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS c 77 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.619A pdb=" N THR c 90 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE c 92 " --> pdb=" O LEU c 88 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 109 removed outlier: 3.526A pdb=" N ARG c 105 " --> pdb=" O GLU c 101 " (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: 3.519A pdb=" N CYS c 167 " --> pdb=" O GLU c 163 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN c 172 " --> pdb=" O HIS c 168 " (cutoff:3.500A) removed outlier: 3.647A 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: 3.838A pdb=" N LEU c 213 " --> pdb=" O GLU c 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE c 214 " --> pdb=" O ARG c 210 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE c 218 " --> pdb=" O PHE c 214 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.676A pdb=" N MET c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 removed outlier: 3.930A pdb=" N GLU c 243 " --> pdb=" O GLY c 239 " (cutoff:3.500A) removed outlier: 3.572A 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 93 through 101 removed outlier: 3.787A pdb=" N SER d 99 " --> pdb=" O ALA d 95 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 115 removed outlier: 3.596A pdb=" N ILE d 106 " --> pdb=" O LYS d 102 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 130 removed outlier: 3.959A pdb=" N ILE d 122 " --> pdb=" O SER d 118 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG d 123 " --> pdb=" O GLN d 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG d 124 " --> pdb=" O VAL d 120 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA d 130 " --> pdb=" O LYS d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 134 through 155 Proline residue: d 138 - end of helix removed outlier: 3.557A pdb=" N ASP d 143 " --> pdb=" O GLU d 139 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS d 149 " --> pdb=" O PHE d 145 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU d 152 " --> pdb=" O ALA d 148 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 4.551A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) removed outlier: 3.694A 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: 5.121A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE d 176 " --> pdb=" O MET d 172 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 removed outlier: 3.613A pdb=" N SER e 82 " --> pdb=" O GLU e 78 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 101 Processing helix chain 'e' and resid 116 through 132 removed outlier: 5.155A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 144 removed outlier: 3.875A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 195 removed outlier: 3.514A pdb=" N ALA e 188 " --> pdb=" O LEU e 184 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU e 192 " --> pdb=" O ALA e 188 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 218 through 223 removed outlier: 6.532A pdb=" N ARG e 222 " --> pdb=" O PRO e 218 " (cutoff:3.500A) removed outlier: 7.059A 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: 4.679A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR e 263 " --> pdb=" O GLU e 259 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 276 removed outlier: 4.017A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL e 272 " --> pdb=" O TYR e 268 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.897A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.338A 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 removed outlier: 3.544A pdb=" N ALA f 103 " --> pdb=" O ASP f 99 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 178 removed outlier: 4.324A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE f 169 " --> pdb=" O THR f 165 " (cutoff:3.500A) Processing helix chain 'f' and resid 200 through 212 removed outlier: 3.606A pdb=" N LEU f 207 " --> pdb=" O GLU f 203 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 52 removed outlier: 4.269A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG g 50 " --> pdb=" O GLN g 46 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU g 52 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 133 removed outlier: 3.967A 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: 3.559A pdb=" N GLU g 163 " --> pdb=" O ALA g 159 " (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: 4.890A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.579A pdb=" N VAL h 126 " --> pdb=" O ARG h 122 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 147 removed outlier: 5.507A 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: 3.774A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.045A 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 removed outlier: 3.515A pdb=" N GLN j 30 " --> pdb=" O GLN j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 41 removed outlier: 4.689A pdb=" N TYR j 40 " --> pdb=" O ASN j 36 " (cutoff:3.500A) removed outlier: 5.631A 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: 3.520A pdb=" N TRP j 91 " --> pdb=" O GLY j 87 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN j 102 " --> pdb=" O LEU j 98 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG j 103 " --> pdb=" O GLN j 99 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS j 104 " --> pdb=" O GLU j 100 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN j 105 " --> pdb=" O GLU j 101 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU j 106 " --> pdb=" O GLN j 102 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN j 107 " --> pdb=" O ARG j 103 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA j 108 " --> pdb=" O LYS j 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 9 removed outlier: 3.783A pdb=" N LEU k 8 " --> pdb=" O ALA k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 39 removed outlier: 3.706A pdb=" N SER k 39 " --> pdb=" O GLN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 47 removed outlier: 3.633A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN k 46 " --> pdb=" O VAL k 42 " (cutoff:3.500A) removed outlier: 3.519A 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: 4.166A pdb=" N ASN l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) removed outlier: 5.340A 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: 3.634A 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: 4.718A pdb=" N GLU l 98 " --> pdb=" O GLU l 94 " (cutoff:3.500A) removed outlier: 4.398A 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: 3.645A pdb=" N LEU l 110 " --> pdb=" O THR l 106 " (cutoff:3.500A) removed outlier: 5.644A 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: 3.657A pdb=" N TRP l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN l 135 " --> pdb=" O ARG l 131 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS l 136 " --> pdb=" O LEU l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 39 removed outlier: 4.710A pdb=" N ALA m 38 " --> pdb=" O ASP m 34 " (cutoff:3.500A) removed outlier: 4.099A 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: 3.730A pdb=" N LYS o 32 " --> pdb=" O SER o 28 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) removed outlier: 4.391A 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: 4.130A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 3.991A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.913A 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: 4.110A pdb=" N LEU p 77 " --> pdb=" O PRO p 73 " (cutoff:3.500A) removed outlier: 5.302A 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 Processing helix chain 'p' and resid 142 through 164 removed outlier: 3.732A pdb=" N THR p 164 " --> pdb=" O GLU p 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 172 through 190 removed outlier: 4.019A pdb=" N ARG p 177 " --> pdb=" O VAL p 173 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG p 179 " --> pdb=" O LEU p 175 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE p 180 " --> pdb=" O HIS p 176 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG p 189 " --> pdb=" O ARG p 185 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 4.133A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 4.082A 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: 4.422A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.524A 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: 3.622A pdb=" N GLU q 84 " --> pdb=" O GLU q 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 164 removed outlier: 3.680A 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: 3.625A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.082A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.806A 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: 3.571A pdb=" N LYS r 114 " --> pdb=" O GLU r 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 183 removed outlier: 4.088A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.236A 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 73 removed outlier: 3.689A pdb=" N TRP s 66 " --> pdb=" O ARG s 62 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR s 69 " --> pdb=" O ARG s 65 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.577A pdb=" N TYR s 108 " --> pdb=" O ARG s 104 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 155 removed outlier: 3.635A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS s 154 " --> pdb=" O LEU s 150 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 169 removed outlier: 4.996A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 171 through 193 Proline residue: s 175 - end of helix removed outlier: 3.713A pdb=" N GLY s 186 " --> pdb=" O SER s 182 " (cutoff:3.500A) Proline residue: s 190 - end of helix Proline residue: s 193 - end of helix Processing helix chain 's' and resid 267 through 272 removed outlier: 4.749A 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: 3.535A pdb=" N ARG s 313 " --> pdb=" O GLU s 309 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN s 315 " --> pdb=" O LEU s 311 " (cutoff:3.500A) Processing helix chain 's' and resid 317 through 344 removed outlier: 5.003A pdb=" N GLU s 321 " --> pdb=" O ALA s 317 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 385 removed outlier: 3.636A pdb=" N GLN s 385 " --> pdb=" O THR s 381 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 3.973A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'u' and resid 107 through 114 removed outlier: 3.550A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY u 129 " --> pdb=" O MET u 180 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'x' and resid 130 through 133 removed outlier: 4.900A pdb=" N ARG x 130 " --> pdb=" O VAL x 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'x' and resid 230 through 236 removed outlier: 3.869A pdb=" N TRP x 236 " --> pdb=" O ASP x 204 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP x 255 " --> pdb=" O LEU x 180 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY x 303 " --> pdb=" O ARG x 382 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER x 311 " --> pdb=" O PRO x 374 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LYS x 379 " --> pdb=" O GLU x 339 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'x' and resid 361 through 365 Processing sheet with id= 5, first strand: chain 'z' and resid 72 through 76 removed outlier: 3.649A pdb=" N ASP z 62 " --> pdb=" O LEU z 75 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN z 164 " --> pdb=" O THR z 185 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '0' and resid 155 through 161 Processing sheet with id= 7, first strand: chain '1' and resid 28 through 34 removed outlier: 6.117A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN 1 15 " --> pdb=" O LEU 1 65 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '1' and resid 41 through 46 removed outlier: 6.191A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '4' and resid 66 through 70 removed outlier: 5.490A pdb=" N HIS 4 98 " --> pdb=" O CYS 4 92 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N CYS 4 92 " --> pdb=" O HIS 4 98 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '5' and resid 126 through 130 removed outlier: 5.309A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '5' and resid 208 through 214 removed outlier: 4.470A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '6' and resid 183 through 187 removed outlier: 3.652A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '6' and resid 189 through 192 removed outlier: 7.144A pdb=" N ARG 6 267 " --> pdb=" O LEU 6 221 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '6' and resid 215 through 218 Processing sheet with id= 15, first strand: chain '6' and resid 272 through 276 removed outlier: 6.924A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR 6 310 " --> pdb=" O ASP 6 276 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '7' and resid 64 through 69 removed outlier: 4.293A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '7' and resid 104 through 107 Processing sheet with id= 18, first strand: chain '7' and resid 164 through 167 removed outlier: 7.457A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '7' and resid 216 through 221 Processing sheet with id= 20, first strand: chain '9' and resid 42 through 45 removed outlier: 3.790A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.569A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLY D 179 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU D 164 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 190 through 194 removed outlier: 4.445A pdb=" N THR D 191 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 193 " --> pdb=" O GLY D 214 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 215 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 139 through 144 Processing sheet with id= 24, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 25, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.834A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'E' and resid 176 through 182 removed outlier: 6.647A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.516A pdb=" N VAL E 206 " --> pdb=" O GLU E 268 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'F' and resid 46 through 50 removed outlier: 3.515A pdb=" N LEU F 79 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 30, first strand: chain 'H' and resid 55 through 58 removed outlier: 7.109A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'H' and resid 94 through 97 Processing sheet with id= 32, first strand: chain 'I' and resid 121 through 125 removed outlier: 5.695A pdb=" N HIS I 150 " --> pdb=" O ASN I 101 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.775A pdb=" N GLY J 18 " --> pdb=" O VAL J 72 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU J 71 " --> pdb=" O GLU J 79 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'K' and resid 55 through 60 removed outlier: 3.599A pdb=" N GLU K 143 " --> pdb=" O TRP K 18 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'K' and resid 77 through 81 removed outlier: 7.355A pdb=" N GLY K 86 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 71 through 76 removed outlier: 4.230A pdb=" N ASP L 71 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS L 83 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER L 102 " --> pdb=" O CYS L 90 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS L 90 " --> pdb=" O SER L 102 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 38, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 39, first strand: chain 'N' and resid 94 through 97 removed outlier: 4.061A pdb=" N HIS N 149 " --> pdb=" O ILE N 131 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.566A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.110A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.650A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Q' and resid 130 through 135 removed outlier: 6.542A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Q' and resid 139 through 143 removed outlier: 3.992A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ARG Q 143 " --> pdb=" O GLY Q 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY Q 146 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 180 through 183 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'S' and resid 105 through 109 removed outlier: 3.552A pdb=" N LEU S 135 " --> pdb=" O VAL S 98 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE S 141 " --> pdb=" O ALA S 138 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 111 through 117 removed outlier: 3.953A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.839A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S' and resid 168 through 175 removed outlier: 3.890A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'T' and resid 65 through 72 removed outlier: 4.802A pdb=" N ALA T 65 " --> pdb=" O GLU T 174 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS T 171 " --> pdb=" O ALA T 137 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'T' and resid 146 through 153 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'U' and resid 38 through 44 removed outlier: 7.072A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA U 67 " --> pdb=" O GLN U 98 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'V' and resid 60 through 65 removed outlier: 4.271A pdb=" N ASP V 60 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL V 76 " --> pdb=" O ASP V 60 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS V 72 " --> pdb=" O ILE V 64 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'V' and resid 78 through 81 removed outlier: 3.828A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 92 through 97 removed outlier: 6.115A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 75 through 78 removed outlier: 6.668A pdb=" N VAL W 133 " --> pdb=" O GLY W 78 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'W' and resid 80 through 84 removed outlier: 7.459A pdb=" N HIS W 80 " --> pdb=" O LEU W 92 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'X' and resid 49 through 53 removed outlier: 5.246A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 85 through 91 Processing sheet with id= 60, first strand: chain 'Y' and resid 165 through 170 removed outlier: 3.555A pdb=" N PHE Y 181 " --> pdb=" O PRO Y 165 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.498A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'a' and resid 45 through 52 removed outlier: 6.104A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'b' and resid 61 through 68 removed outlier: 3.664A pdb=" N ARG b 74 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER b 88 " --> pdb=" O PRO b 73 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL b 75 " --> pdb=" O GLU b 86 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU b 86 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA b 77 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL b 84 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYR b 79 " --> pdb=" O GLY b 82 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 65, first strand: chain 'c' and resid 269 through 274 removed outlier: 4.015A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'd' and resid 212 through 219 removed outlier: 6.647A pdb=" N TYR d 245 " --> pdb=" O LYS d 264 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS d 264 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'e' and resid 174 through 178 removed outlier: 6.152A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU e 157 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'e' and resid 197 through 201 removed outlier: 7.569A pdb=" N GLU e 197 " --> pdb=" O SER e 244 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN e 199 " --> pdb=" O ASP e 242 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR e 240 " --> pdb=" O GLU e 201 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'e' and resid 211 through 216 removed outlier: 3.995A pdb=" N GLY e 211 " --> pdb=" O PHE e 233 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE e 215 " --> pdb=" O ALA e 229 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'e' and resid 44 through 53 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 'f' and resid 144 through 147 removed outlier: 7.043A pdb=" N VAL f 134 " --> pdb=" O ASP f 147 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.624A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'h' and resid 58 through 61 removed outlier: 6.683A pdb=" N ARG h 58 " --> pdb=" O ASP h 136 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP h 136 " --> pdb=" O ARG h 58 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'k' and resid 49 through 56 removed outlier: 3.629A pdb=" N SER k 50 " --> pdb=" O LYS k 14 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'm' and resid 62 through 67 removed outlier: 4.611A pdb=" N SER m 62 " --> pdb=" O LYS m 58 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'p' and resid 79 through 83 Processing sheet with id= 77, first strand: chain 'r' and resid 35 through 42 Processing sheet with id= 78, first strand: chain 's' and resid 90 through 93 removed outlier: 4.079A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 's' and resid 112 through 116 removed outlier: 6.405A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 's' and resid 198 through 202 removed outlier: 3.525A pdb=" N GLN s 240 " --> pdb=" O ASP s 201 " (cutoff:3.500A) 2861 hydrogen bonds defined for protein. 8493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 722 hydrogen bonds 1240 hydrogen bond angles 0 basepair planarities 305 basepair parallelities 802 stacking parallelities Total time for adding SS restraints: 61.57 Time building geometry restraints manager: 39.13 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: 45196 1.41 - 1.61: 66814 1.61 - 1.80: 1693 1.80 - 2.00: 121 2.00 - 2.20: 4 Bond restraints: 113828 Sorted by residual: bond pdb=" C1' SAM x 401 " pdb=" C2' SAM x 401 " ideal model delta sigma weight residual 1.307 1.519 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C1' SAM x 401 " pdb=" O4' SAM x 401 " ideal model delta sigma weight residual 1.616 1.414 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C2 OMU A3039 " pdb=" N3 OMU A3039 " ideal model delta sigma weight residual 1.499 1.338 0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" C34 PM8 w 200 " pdb=" N36 PM8 w 200 " ideal model delta sigma weight residual 1.451 1.326 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C6 SAM x 401 " pdb=" N6 SAM x 401 " ideal model delta sigma weight residual 1.452 1.329 0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 113823 not shown) Histogram of bond angle deviations from ideal: 74.68 - 86.54: 2 86.54 - 98.41: 0 98.41 - 110.28: 38570 110.28 - 122.15: 100357 122.15 - 134.01: 22207 Bond angle restraints: 161136 Sorted by residual: angle pdb=" N VAL P 61 " pdb=" CA VAL P 61 " pdb=" C VAL P 61 " ideal model delta sigma weight residual 113.47 108.93 4.54 1.01e+00 9.80e-01 2.02e+01 angle pdb=" C LYS L 120 " pdb=" N THR L 121 " pdb=" CA THR L 121 " ideal model delta sigma weight residual 120.67 126.48 -5.81 1.34e+00 5.57e-01 1.88e+01 angle pdb=" N VAL I 130 " pdb=" CA VAL I 130 " pdb=" C VAL I 130 " ideal model delta sigma weight residual 112.96 108.86 4.10 1.00e+00 1.00e+00 1.68e+01 angle pdb=" N1 SAM x 401 " pdb=" C6 SAM x 401 " pdb=" N6 SAM x 401 " ideal model delta sigma weight residual 109.25 120.19 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" C1' SAM x 401 " pdb=" N9 SAM x 401 " pdb=" C8 SAM x 401 " ideal model delta sigma weight residual 115.64 126.50 -10.86 3.00e+00 1.11e-01 1.31e+01 ... (remaining 161131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 66226 35.98 - 71.95: 2302 71.95 - 107.93: 450 107.93 - 143.91: 12 143.91 - 179.88: 23 Dihedral angle restraints: 69013 sinusoidal: 41699 harmonic: 27314 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 200.00 27.34 172.66 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C A2079 " pdb=" C1' C A2079 " pdb=" N1 C A2079 " pdb=" C2 C A2079 " ideal model delta sinusoidal sigma weight residual -160.00 7.13 -167.13 1 1.50e+01 4.44e-03 8.43e+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 34.80 165.20 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 69010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 16508 0.044 - 0.088: 1556 0.088 - 0.133: 677 0.133 - 0.177: 8 0.177 - 0.221: 1 Chirality restraints: 18750 Sorted by residual: chirality pdb=" C3' A A2457 " pdb=" C4' A A2457 " pdb=" O3' A A2457 " pdb=" C2' A A2457 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1' U A2499 " pdb=" O4' U A2499 " pdb=" C2' U A2499 " pdb=" N1 U A2499 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.71e-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 -2.31 -0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 18747 not shown) Planarity restraints: 15199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' N A3244 " -0.402 2.00e-02 2.50e+03 4.22e-01 3.56e+03 pdb=" C2' N A3244 " -0.428 2.00e-02 2.50e+03 pdb=" C3' N A3244 " -0.505 2.00e-02 2.50e+03 pdb=" C4' N A3244 " 0.381 2.00e-02 2.50e+03 pdb=" C5' N A3244 " 0.110 2.00e-02 2.50e+03 pdb=" O2' N A3244 " 0.799 2.00e-02 2.50e+03 pdb=" O3' N A3244 " -0.092 2.00e-02 2.50e+03 pdb=" O4' N A3244 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N A3240 " -0.402 2.00e-02 2.50e+03 4.20e-01 3.53e+03 pdb=" C2' N A3240 " -0.433 2.00e-02 2.50e+03 pdb=" C3' N A3240 " -0.503 2.00e-02 2.50e+03 pdb=" C4' N A3240 " 0.383 2.00e-02 2.50e+03 pdb=" C5' N A3240 " 0.101 2.00e-02 2.50e+03 pdb=" O2' N A3240 " 0.790 2.00e-02 2.50e+03 pdb=" O3' N A3240 " -0.083 2.00e-02 2.50e+03 pdb=" O4' N A3240 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N A3236 " 0.400 2.00e-02 2.50e+03 4.20e-01 3.53e+03 pdb=" C2' N A3236 " 0.430 2.00e-02 2.50e+03 pdb=" C3' N A3236 " 0.503 2.00e-02 2.50e+03 pdb=" C4' N A3236 " -0.381 2.00e-02 2.50e+03 pdb=" C5' N A3236 " -0.107 2.00e-02 2.50e+03 pdb=" O2' N A3236 " -0.793 2.00e-02 2.50e+03 pdb=" O3' N A3236 " 0.088 2.00e-02 2.50e+03 pdb=" O4' N A3236 " -0.140 2.00e-02 2.50e+03 ... (remaining 15196 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.64: 1510 2.64 - 3.26: 104109 3.26 - 3.89: 227506 3.89 - 4.51: 313487 4.51 - 5.14: 450100 Nonbonded interactions: 1096712 Sorted by model distance: nonbonded pdb=" O2 C A3009 " pdb="MG MG A3382 " model vdw 2.009 2.170 nonbonded pdb=" OP1 U A3037 " pdb="MG MG A3331 " model vdw 2.024 2.170 nonbonded pdb=" O4 U A2475 " pdb="MG MG A3331 " model vdw 2.025 2.170 nonbonded pdb=" O4 U A1758 " pdb="MG MG A3302 " model vdw 2.025 2.170 nonbonded pdb=" OP2 A A2504 " pdb="MG MG A3309 " model vdw 2.027 2.170 ... (remaining 1096707 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: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 21.140 Check model and map are aligned: 1.230 Set scattering table: 0.730 Process input model: 318.940 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 352.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.212 113828 Z= 0.156 Angle : 0.403 10.941 161136 Z= 0.222 Chirality : 0.031 0.221 18750 Planarity : 0.019 0.422 15199 Dihedral : 15.654 179.885 51327 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.51 % Allowed : 1.69 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.91 (0.09), residues: 9235 helix: 0.84 (0.09), residues: 3148 sheet: 0.40 (0.14), residues: 1286 loop : 0.69 (0.09), residues: 4801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP s 346 HIS 0.003 0.000 HIS W 76 PHE 0.008 0.001 PHE s 283 TYR 0.013 0.001 TYR y 181 ARG 0.003 0.000 ARG u 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1592 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1550 time to evaluate : 7.221 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 17 residues processed: 1583 average time/residue: 1.0738 time to fit residues: 2786.0411 Evaluate side-chains 801 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 784 time to evaluate : 7.389 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.8730 time to fit residues: 35.8262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 900 optimal weight: 50.0000 chunk 808 optimal weight: 9.9990 chunk 448 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 432 optimal weight: 7.9990 chunk 836 optimal weight: 30.0000 chunk 323 optimal weight: 20.0000 chunk 508 optimal weight: 9.9990 chunk 622 optimal weight: 8.9990 chunk 968 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 GLN ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 172 GLN x 214 GLN x 230 GLN ** x 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 304 HIS ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 122 GLN y 123 GLN y 192 GLN y 210 GLN y 235 GLN y 255 GLN ** z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 136 GLN ** z 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 163 GLN z 186 GLN ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 170 GLN 1 31 ASN 3 154 GLN ** 3 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 96 HIS ** 5 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 266 HIS ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 320 GLN 6 354 GLN 7 45 ASN 7 69 HIS 7 198 ASN 7 290 GLN ** 8 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN F 103 GLN F 105 ASN F 138 HIS F 188 HIS F 201 GLN F 241 ASN I 36 HIS I 43 GLN K 56 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 153 ASN M 289 ASN O 27 HIS ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 ASN P 79 HIS ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN R 149 HIS ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN T 95 GLN T 119 GLN T 126 HIS U 27 GLN U 136 GLN V 119 GLN ** X 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 147 GLN Y 183 GLN Z 64 HIS Z 67 HIS b 149 GLN c 73 GLN c 222 GLN d 196 GLN d 205 GLN d 262 HIS d 286 GLN e 67 GLN e 75 GLN e 251 HIS ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 GLN f 189 HIS g 63 HIS g 93 ASN h 67 GLN ** h 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 82 GLN l 124 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 85 HIS ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN p 194 HIS q 81 GLN q 107 GLN q 142 ASN s 239 ASN ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 358 GLN s 385 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 113828 Z= 0.550 Angle : 0.914 18.424 161136 Z= 0.493 Chirality : 0.049 0.330 18750 Planarity : 0.008 0.108 15199 Dihedral : 19.031 179.526 31603 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.41 % Allowed : 8.13 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.08), residues: 9235 helix: 0.27 (0.09), residues: 3268 sheet: -0.09 (0.14), residues: 1281 loop : 0.04 (0.09), residues: 4686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP V 215 HIS 0.013 0.002 HIS 7 232 PHE 0.033 0.003 PHE N 175 TYR 0.033 0.003 TYR 5 176 ARG 0.010 0.001 ARG K 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 818 time to evaluate : 7.400 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 outliers start: 199 outliers final: 133 residues processed: 958 average time/residue: 0.9942 time to fit residues: 1627.8717 Evaluate side-chains 808 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 675 time to evaluate : 7.405 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 0 residues processed: 133 average time/residue: 0.8052 time to fit residues: 208.6539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 538 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 chunk 806 optimal weight: 20.0000 chunk 659 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 970 optimal weight: 10.0000 chunk 1048 optimal weight: 2.9990 chunk 864 optimal weight: 10.0000 chunk 962 optimal weight: 8.9990 chunk 330 optimal weight: 4.9990 chunk 778 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 105 HIS ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 316 GLN ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 150 GLN 0 96 ASN 3 170 ASN 4 95 HIS ** 5 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 380 GLN ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 177 HIS D 252 HIS F 74 GLN F 105 ASN F 201 GLN L 48 ASN O 100 GLN P 97 GLN ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 56 GLN T 145 GLN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN V 119 GLN X 172 GLN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN q 147 GLN ** s 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 113828 Z= 0.265 Angle : 0.704 17.454 161136 Z= 0.394 Chirality : 0.040 0.269 18750 Planarity : 0.007 0.109 15199 Dihedral : 18.938 179.680 31603 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.15 % Allowed : 9.49 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.08), residues: 9235 helix: 0.71 (0.09), residues: 3240 sheet: -0.10 (0.14), residues: 1257 loop : 0.09 (0.09), residues: 4738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP V 170 HIS 0.010 0.001 HIS L 52 PHE 0.027 0.002 PHE N 175 TYR 0.032 0.002 TYR x 52 ARG 0.011 0.001 ARG u 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 764 time to evaluate : 7.747 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 outliers start: 95 outliers final: 38 residues processed: 828 average time/residue: 1.0336 time to fit residues: 1467.4858 Evaluate side-chains 714 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 676 time to evaluate : 7.400 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.8224 time to fit residues: 68.1524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 959 optimal weight: 1.9990 chunk 729 optimal weight: 10.0000 chunk 503 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 463 optimal weight: 0.0870 chunk 651 optimal weight: 10.0000 chunk 974 optimal weight: 2.9990 chunk 1031 optimal weight: 0.9990 chunk 508 optimal weight: 8.9990 chunk 923 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 277 GLN ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN F 74 GLN F 105 ASN I 36 HIS O 100 GLN P 97 GLN ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 145 GLN V 119 GLN e 67 GLN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN h 118 HIS k 15 GLN l 124 GLN l 130 ASN p 53 GLN ** s 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 113828 Z= 0.159 Angle : 0.644 17.038 161136 Z= 0.367 Chirality : 0.037 0.278 18750 Planarity : 0.006 0.108 15199 Dihedral : 18.829 179.576 31603 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.05 % Allowed : 10.06 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.70 (0.09), residues: 9235 helix: 1.13 (0.09), residues: 3231 sheet: -0.02 (0.14), residues: 1232 loop : 0.26 (0.09), residues: 4772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP V 170 HIS 0.005 0.001 HIS L 52 PHE 0.027 0.001 PHE f 170 TYR 0.032 0.001 TYR 9 76 ARG 0.006 0.000 ARG k 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 741 time to evaluate : 7.448 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 outliers start: 87 outliers final: 39 residues processed: 797 average time/residue: 0.9966 time to fit residues: 1364.0312 Evaluate side-chains 709 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 670 time to evaluate : 7.417 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.7924 time to fit residues: 67.6197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 858 optimal weight: 9.9990 chunk 585 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 chunk 767 optimal weight: 9.9990 chunk 425 optimal weight: 0.5980 chunk 880 optimal weight: 5.9990 chunk 712 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 526 optimal weight: 8.9990 chunk 925 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 105 HIS ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 177 HIS D 221 ASN D 271 ASN F 74 GLN K 9 GLN ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 HIS T 95 GLN T 145 GLN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 GLN p 53 GLN r 69 GLN r 146 GLN s 239 ASN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 113828 Z= 0.298 Angle : 0.708 17.105 161136 Z= 0.394 Chirality : 0.040 0.283 18750 Planarity : 0.007 0.109 15199 Dihedral : 18.893 179.239 31603 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.19 % Allowed : 10.83 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.49 (0.08), residues: 9235 helix: 0.97 (0.09), residues: 3250 sheet: -0.06 (0.14), residues: 1269 loop : 0.10 (0.09), residues: 4716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP V 170 HIS 0.013 0.001 HIS x 105 PHE 0.026 0.002 PHE N 175 TYR 0.022 0.002 TYR 5 176 ARG 0.010 0.001 ARG F 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 694 time to evaluate : 7.430 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 outliers start: 98 outliers final: 50 residues processed: 758 average time/residue: 1.0088 time to fit residues: 1313.5766 Evaluate side-chains 702 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 652 time to evaluate : 7.477 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.7880 time to fit residues: 84.3418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 346 optimal weight: 8.9990 chunk 928 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 chunk 605 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 1032 optimal weight: 5.9990 chunk 856 optimal weight: 40.0000 chunk 477 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 341 optimal weight: 10.0000 chunk 541 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 234 HIS ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 177 HIS E 281 ASN I 36 HIS K 9 GLN O 100 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 253 GLN ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS p 53 GLN r 146 GLN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 113828 Z= 0.320 Angle : 0.724 17.055 161136 Z= 0.401 Chirality : 0.041 0.287 18750 Planarity : 0.007 0.109 15199 Dihedral : 18.956 179.566 31603 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.05 % Allowed : 11.59 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.08), residues: 9235 helix: 0.83 (0.09), residues: 3271 sheet: -0.18 (0.14), residues: 1277 loop : -0.05 (0.09), residues: 4687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP V 170 HIS 0.009 0.001 HIS s 296 PHE 0.034 0.002 PHE 6 273 TYR 0.022 0.002 TYR 5 176 ARG 0.010 0.001 ARG y 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 703 time to evaluate : 7.481 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 outliers start: 87 outliers final: 51 residues processed: 762 average time/residue: 0.9997 time to fit residues: 1311.1423 Evaluate side-chains 701 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 650 time to evaluate : 6.659 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.7260 time to fit residues: 78.3481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 995 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 588 optimal weight: 0.9980 chunk 753 optimal weight: 2.9990 chunk 584 optimal weight: 10.0000 chunk 869 optimal weight: 30.0000 chunk 576 optimal weight: 5.9990 chunk 1028 optimal weight: 9.9990 chunk 643 optimal weight: 5.9990 chunk 626 optimal weight: 3.9990 chunk 474 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 203 ASN x 288 GLN ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 45 ASN ** 5 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN O 100 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 253 GLN ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 145 GLN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 GLN k 72 HIS o 46 HIS p 53 GLN ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 113828 Z= 0.180 Angle : 0.655 16.883 161136 Z= 0.371 Chirality : 0.037 0.262 18750 Planarity : 0.006 0.108 15199 Dihedral : 18.867 179.920 31603 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.56 % Allowed : 12.12 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.60 (0.09), residues: 9235 helix: 1.17 (0.09), residues: 3255 sheet: -0.14 (0.14), residues: 1286 loop : 0.13 (0.09), residues: 4694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 85 HIS 0.008 0.001 HIS h 110 PHE 0.026 0.001 PHE 9 128 TYR 0.020 0.001 TYR f 98 ARG 0.006 0.000 ARG h 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 712 time to evaluate : 7.488 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 outliers start: 46 outliers final: 22 residues processed: 740 average time/residue: 1.0238 time to fit residues: 1301.5133 Evaluate side-chains 681 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 659 time to evaluate : 7.447 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.8155 time to fit residues: 43.0772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 636 optimal weight: 8.9990 chunk 410 optimal weight: 9.9990 chunk 614 optimal weight: 6.9990 chunk 309 optimal weight: 30.0000 chunk 202 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 653 optimal weight: 8.9990 chunk 700 optimal weight: 1.9990 chunk 508 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 808 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 177 HIS F 74 GLN I 36 HIS K 9 GLN ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 253 GLN ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 GLN T 145 GLN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN ** e 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN p 146 ASN q 137 GLN ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 146 GLN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 113828 Z= 0.373 Angle : 0.766 17.179 161136 Z= 0.420 Chirality : 0.043 0.302 18750 Planarity : 0.007 0.109 15199 Dihedral : 19.015 179.734 31603 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.75 % Allowed : 12.67 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.17 (0.08), residues: 9235 helix: 0.75 (0.09), residues: 3269 sheet: -0.23 (0.14), residues: 1274 loop : -0.14 (0.09), residues: 4692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP V 170 HIS 0.010 0.001 HIS s 296 PHE 0.035 0.002 PHE 6 273 TYR 0.024 0.002 TYR a 43 ARG 0.009 0.001 ARG h 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 675 time to evaluate : 7.528 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 outliers start: 62 outliers final: 36 residues processed: 712 average time/residue: 1.0210 time to fit residues: 1244.6193 Evaluate side-chains 674 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 638 time to evaluate : 6.680 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.7315 time to fit residues: 58.1406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 935 optimal weight: 8.9990 chunk 985 optimal weight: 1.9990 chunk 898 optimal weight: 9.9990 chunk 958 optimal weight: 7.9990 chunk 984 optimal weight: 9.9990 chunk 576 optimal weight: 0.9990 chunk 417 optimal weight: 2.9990 chunk 752 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 866 optimal weight: 8.9990 chunk 906 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 223 HIS K 9 GLN N 178 GLN O 100 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 253 GLN ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN e 219 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 113828 Z= 0.233 Angle : 0.690 16.944 161136 Z= 0.387 Chirality : 0.038 0.275 18750 Planarity : 0.007 0.109 15199 Dihedral : 18.934 179.233 31603 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.42 % Allowed : 13.00 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.33 (0.09), residues: 9235 helix: 0.94 (0.09), residues: 3278 sheet: -0.20 (0.14), residues: 1277 loop : -0.06 (0.09), residues: 4680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP q 143 HIS 0.006 0.001 HIS s 296 PHE 0.025 0.001 PHE 9 128 TYR 0.027 0.001 TYR u 141 ARG 0.007 0.000 ARG F 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 670 time to evaluate : 7.550 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 outliers start: 35 outliers final: 23 residues processed: 686 average time/residue: 1.0248 time to fit residues: 1207.7202 Evaluate side-chains 671 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 648 time to evaluate : 7.446 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.9755 time to fit residues: 49.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 955 optimal weight: 10.0000 chunk 629 optimal weight: 5.9990 chunk 1013 optimal weight: 0.5980 chunk 618 optimal weight: 10.0000 chunk 480 optimal weight: 8.9990 chunk 704 optimal weight: 4.9990 chunk 1063 optimal weight: 0.9980 chunk 978 optimal weight: 4.9990 chunk 846 optimal weight: 0.0770 chunk 87 optimal weight: 0.1980 chunk 653 optimal weight: 3.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 191 GLN ** 5 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN I 36 HIS ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN O 147 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN Z 53 HIS d 217 HIS ** e 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 GLN f 112 ASN k 72 HIS ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 53 GLN p 146 ASN ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 113828 Z= 0.147 Angle : 0.649 16.911 161136 Z= 0.367 Chirality : 0.036 0.252 18750 Planarity : 0.006 0.108 15199 Dihedral : 18.800 179.728 31603 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.19 % Allowed : 13.30 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.67 (0.09), residues: 9235 helix: 1.28 (0.09), residues: 3253 sheet: -0.09 (0.14), residues: 1279 loop : 0.13 (0.09), residues: 4703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP q 143 HIS 0.007 0.001 HIS u 136 PHE 0.049 0.001 PHE u 140 TYR 0.035 0.001 TYR u 141 ARG 0.007 0.000 ARG F 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18470 Ramachandran restraints generated. 9235 Oldfield, 0 Emsley, 9235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 704 time to evaluate : 7.527 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 outliers start: 16 outliers final: 6 residues processed: 711 average time/residue: 1.0303 time to fit residues: 1257.5530 Evaluate side-chains 676 residues out of total 8273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 670 time to evaluate : 7.437 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.8516 time to fit residues: 18.8446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1067 random chunks: chunk 519 optimal weight: 40.0000 chunk 672 optimal weight: 5.9990 chunk 901 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 780 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 847 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 870 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 136 HIS ** v 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 158 GLN ** 5 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN H 121 ASN K 9 GLN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 GLN ** P 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 72 HIS ** o 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.101206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.078384 restraints weight = 350542.930| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.21 r_work: 0.3422 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 113828 Z= 0.228 Angle : 0.680 17.057 161136 Z= 0.381 Chirality : 0.038 0.270 18750 Planarity : 0.007 0.109 15199 Dihedral : 18.797 179.703 31603 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.27 % Allowed : 13.64 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.60 (0.09), residues: 9235 helix: 1.21 (0.09), residues: 3252 sheet: -0.13 (0.14), residues: 1301 loop : 0.09 (0.09), residues: 4682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP V 85 HIS 0.006 0.001 HIS u 136 PHE 0.024 0.001 PHE N 175 TYR 0.027 0.001 TYR u 141 ARG 0.018 0.000 ARG q 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26553.82 seconds wall clock time: 468 minutes 29.57 seconds (28109.57 seconds total)