Starting phenix.real_space_refine on Sat Mar 2 01:56:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7a_24296/03_2024/7r7a_24296.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7a_24296/03_2024/7r7a_24296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7a_24296/03_2024/7r7a_24296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7a_24296/03_2024/7r7a_24296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7a_24296/03_2024/7r7a_24296.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7a_24296/03_2024/7r7a_24296.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2815 5.49 5 S 269 5.16 5 C 85832 2.51 5 N 27710 2.21 5 O 36459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153087 Number of models: 1 Model: "" Number of chains: 59 Chain: "1" Number of atoms: 55024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2571, 55024 Inner-chain residues flagged as termini: ['pdbres=" A 12404 "'] Classifications: {'RNA': 2571} Modifications used: {'5*END': 1, 'rna2p_pur': 254, 'rna2p_pyr': 174, 'rna3p_pur': 1175, 'rna3p_pyr': 968} Link IDs: {'rna2p': 428, 'rna3p': 2142} Chain breaks: 18 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 32, 'rna3p': 125} Chain: "7" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1048 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Chain: "A" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2174 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain: "B" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2661 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2731 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Chain: "E" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1309 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 154} Chain breaks: 1 Chain: "F" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "H" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1510 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "J" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1215 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "L" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 991 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "N" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1621 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain breaks: 1 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1442 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain: "Q" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1035 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "S" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1432 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 401 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1870 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "X" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1068 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "b" Number of atoms: 4066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4066 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 23, 'TRANS': 478} Chain breaks: 3 Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "e" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1009 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 628 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain breaks: 1 Chain: "j" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 580 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'TRANS': 71} Chain: "l" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1394 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "m" Number of atoms: 5377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5377 Classifications: {'peptide': 666} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 618} Chain breaks: 3 Chain: "q" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2799 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 16, 'TRANS': 341} Chain: "r" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1438 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "s" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "u" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1183 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "v" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1087 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain breaks: 2 Chain: "y" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "8" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3567 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 16, 'TRANS': 453} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 102 Chain: "I" Number of atoms: 4247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4247 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 19, 'TRANS': 513} Chain: "K" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2274 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 2 Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "R" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "G" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1549 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain breaks: 1 Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "n" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3470 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 402} Chain breaks: 3 Chain: "p" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2628 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 10, 'TRANS': 326} Chain breaks: 2 Chain: "t" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2293 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 2 Chain: "6" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1838 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 20, 'rna3p_pur': 30, 'rna3p_pyr': 27} Link IDs: {'rna2p': 30, 'rna3p': 56} Chain breaks: 1 Chain: "D" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3451 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 21, 'TRANS': 410} Chain breaks: 2 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "w" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3446 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 7, 'TRANS': 414} Chain breaks: 7 Chain: "a" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1695 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 204} Chain: "x" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4340 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 94711 SG CYS j 19 152.764 181.484 172.390 1.00 7.64 S ATOM 94736 SG CYS j 22 155.678 181.812 169.980 1.00 7.32 S ATOM 94836 SG CYS j 34 153.824 178.515 170.267 1.00 5.54 S ATOM 94854 SG CYS j 37 156.050 179.713 173.111 1.00 5.77 S ATOM A0LCQ SG CYS g 44 97.234 175.977 193.296 1.00 8.19 S ATOM A0LD8 SG CYS g 47 95.091 174.087 190.831 1.00 10.46 S ATOM A0LKA SG CYS g 81 93.440 176.407 193.294 1.00 9.46 S ATOM A0LKT SG CYS g 84 94.728 173.215 194.542 1.00 9.87 S Residues with excluded nonbonded symmetry interactions: 203 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 191 not shown) Time building chain proxies: 54.94, per 1000 atoms: 0.36 Number of scatterers: 153087 At special positions: 0 Unit cell: (268.92, 266.76, 326.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 269 16.00 P 2815 15.00 O 36459 8.00 N 27710 7.00 C 85832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.93 Conformation dependent library (CDL) restraints added in 12.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " Number of angles added : 12 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22050 Finding SS restraints... Secondary structure from input PDB file: 464 helices and 104 sheets defined 45.7% alpha, 12.6% beta 830 base pairs and 1418 stacking pairs defined. Time for finding SS restraints: 44.33 Creating SS restraints... Processing helix chain '7' and resid 23 through 28 Processing helix chain '7' and resid 46 through 60 Processing helix chain '7' and resid 104 through 116 removed outlier: 4.042A pdb=" N LEU 7 108 " --> pdb=" O ASP 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 125 through 146 removed outlier: 3.598A pdb=" N ILE 7 136 " --> pdb=" O ARG 7 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.783A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 146 through 161 removed outlier: 3.644A pdb=" N ASN A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.549A pdb=" N ASP A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 244 through 278 removed outlier: 3.506A pdb=" N LYS A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.886A pdb=" N LEU A 289 " --> pdb=" O ASN A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.747A pdb=" N PHE B 16 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 17' Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.900A pdb=" N LYS B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 116' Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.939A pdb=" N GLU B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.940A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 154 through 157 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.709A pdb=" N VAL C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.509A pdb=" N LEU C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.511A pdb=" N ILE C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 328 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.263A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 360 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.505A pdb=" N PHE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.725A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 27 through 72 Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.644A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.989A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS F 128 " --> pdb=" O LEU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.878A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 235 through 244 removed outlier: 3.545A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 67 through 84 Processing helix chain 'H' and resid 116 through 120 removed outlier: 3.825A pdb=" N GLY H 119 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.864A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 209 Processing helix chain 'J' and resid 240 through 264 removed outlier: 3.519A pdb=" N LEU J 244 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP J 252 " --> pdb=" O LYS J 248 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 253 " --> pdb=" O GLN J 249 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 314 removed outlier: 3.917A pdb=" N LYS J 287 " --> pdb=" O GLU J 283 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU J 303 " --> pdb=" O LYS J 299 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN J 310 " --> pdb=" O ARG J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 339 removed outlier: 3.582A pdb=" N ILE J 337 " --> pdb=" O THR J 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 20 removed outlier: 3.537A pdb=" N GLU L 20 " --> pdb=" O HIS L 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 20' Processing helix chain 'L' and resid 27 through 44 Processing helix chain 'L' and resid 76 through 83 Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' Processing helix chain 'L' and resid 105 through 120 removed outlier: 3.554A pdb=" N TYR L 119 " --> pdb=" O ARG L 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 88 Processing helix chain 'M' and resid 90 through 96 Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 136 removed outlier: 3.520A pdb=" N MET M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 31 Processing helix chain 'N' and resid 44 through 52 removed outlier: 3.512A pdb=" N ARG N 49 " --> pdb=" O PRO N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.541A pdb=" N THR N 101 " --> pdb=" O SER N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 153 through 157 Processing helix chain 'N' and resid 158 through 162 Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 177 through 181 removed outlier: 3.714A pdb=" N PHE N 180 " --> pdb=" O GLY N 177 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN N 181 " --> pdb=" O HIS N 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 177 through 181' Processing helix chain 'N' and resid 186 through 195 Processing helix chain 'O' and resid 15 through 29 removed outlier: 3.670A pdb=" N LEU O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 59 Processing helix chain 'O' and resid 75 through 86 removed outlier: 3.517A pdb=" N ALA O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 100 Processing helix chain 'O' and resid 111 through 115 removed outlier: 3.514A pdb=" N LYS O 114 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 144 removed outlier: 3.642A pdb=" N SER O 144 " --> pdb=" O LYS O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 185 removed outlier: 3.771A pdb=" N GLU O 166 " --> pdb=" O VAL O 162 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 197 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 35 Processing helix chain 'P' and resid 40 through 53 removed outlier: 3.729A pdb=" N ASP P 53 " --> pdb=" O GLU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 77 removed outlier: 3.830A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'P' and resid 169 through 183 removed outlier: 3.663A pdb=" N ILE P 182 " --> pdb=" O ALA P 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 44 through 52 Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'S' and resid 33 through 48 Processing helix chain 'S' and resid 98 through 115 Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 131 through 135 Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'T' and resid 102 through 121 removed outlier: 3.630A pdb=" N ALA T 114 " --> pdb=" O LYS T 110 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 37 removed outlier: 4.222A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR W 37 " --> pdb=" O ALA W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 60 removed outlier: 4.160A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 removed outlier: 3.563A pdb=" N LEU W 77 " --> pdb=" O LEU W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 96 removed outlier: 3.758A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 removed outlier: 3.502A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 160 No H-bonds generated for 'chain 'W' and resid 158 through 160' Processing helix chain 'W' and resid 161 through 168 removed outlier: 3.617A pdb=" N MET W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'X' and resid 4 through 16 removed outlier: 3.575A pdb=" N THR X 8 " --> pdb=" O SER X 4 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 69 through 80 removed outlier: 3.557A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP X 78 " --> pdb=" O LYS X 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN X 80 " --> pdb=" O VAL X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 removed outlier: 3.579A pdb=" N LYS X 100 " --> pdb=" O LYS X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 137 Processing helix chain 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 4.262A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 74 through 78 removed outlier: 3.529A pdb=" N LYS Y 77 " --> pdb=" O TYR Y 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'b' and resid 13 through 28 Processing helix chain 'b' and resid 38 through 68 removed outlier: 3.708A pdb=" N LYS b 49 " --> pdb=" O PHE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 117 removed outlier: 3.560A pdb=" N ILE b 98 " --> pdb=" O SER b 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 142 Processing helix chain 'b' and resid 143 through 159 removed outlier: 3.783A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 235 through 246 removed outlier: 3.920A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 258 through 262 removed outlier: 3.649A pdb=" N PHE b 262 " --> pdb=" O GLN b 259 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 274 Processing helix chain 'b' and resid 275 through 279 removed outlier: 3.505A pdb=" N ALA b 279 " --> pdb=" O PRO b 276 " (cutoff:3.500A) Processing helix chain 'b' and resid 303 through 308 removed outlier: 4.501A pdb=" N GLU b 307 " --> pdb=" O ALA b 303 " (cutoff:3.500A) Processing helix chain 'b' and resid 326 through 341 removed outlier: 3.654A pdb=" N GLU b 330 " --> pdb=" O GLU b 326 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 384 removed outlier: 3.617A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 406 Processing helix chain 'b' and resid 415 through 419 removed outlier: 3.517A pdb=" N ASP b 418 " --> pdb=" O ASN b 415 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS b 419 " --> pdb=" O LEU b 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 415 through 419' Processing helix chain 'b' and resid 424 through 430 removed outlier: 3.578A pdb=" N LYS b 428 " --> pdb=" O ASP b 425 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN b 429 " --> pdb=" O GLU b 426 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP b 430 " --> pdb=" O TRP b 427 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 445 Processing helix chain 'b' and resid 448 through 466 removed outlier: 3.981A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 511 removed outlier: 3.629A pdb=" N LYS b 490 " --> pdb=" O VAL b 486 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU b 491 " --> pdb=" O ASP b 487 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS b 492 " --> pdb=" O ASP b 488 " (cutoff:3.500A) Processing helix chain 'b' and resid 520 through 524 Processing helix chain 'b' and resid 528 through 539 removed outlier: 3.807A pdb=" N GLU b 533 " --> pdb=" O GLY b 529 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 45 removed outlier: 3.761A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS d 43 " --> pdb=" O PHE d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 removed outlier: 3.533A pdb=" N GLN d 57 " --> pdb=" O PRO d 53 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.699A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'f' and resid 43 through 45 No H-bonds generated for 'chain 'f' and resid 43 through 45' Processing helix chain 'f' and resid 90 through 94 removed outlier: 3.732A pdb=" N PHE f 94 " --> pdb=" O ALA f 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 10 removed outlier: 3.517A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 36 removed outlier: 3.609A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 70 removed outlier: 3.851A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 91 Processing helix chain 'h' and resid 93 through 98 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.596A pdb=" N GLU i 46 " --> pdb=" O SER i 42 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 63 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 99 removed outlier: 3.662A pdb=" N ALA i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 51 through 56 removed outlier: 3.563A pdb=" N ARG j 56 " --> pdb=" O LYS j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 76 removed outlier: 3.657A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 18 Processing helix chain 'l' and resid 23 through 28 removed outlier: 3.966A pdb=" N VAL l 28 " --> pdb=" O SER l 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 54 removed outlier: 3.968A pdb=" N LEU l 54 " --> pdb=" O HIS l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 58 removed outlier: 3.573A pdb=" N VAL l 58 " --> pdb=" O ALA l 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 55 through 58' Processing helix chain 'l' and resid 59 through 61 No H-bonds generated for 'chain 'l' and resid 59 through 61' Processing helix chain 'l' and resid 85 through 92 removed outlier: 3.523A pdb=" N HIS l 92 " --> pdb=" O VAL l 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 103 through 109 removed outlier: 3.504A pdb=" N PHE l 107 " --> pdb=" O GLY l 103 " (cutoff:3.500A) Processing helix chain 'l' and resid 171 through 176 removed outlier: 3.814A pdb=" N ASP l 175 " --> pdb=" O GLU l 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU l 176 " --> pdb=" O TYR l 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 171 through 176' Processing helix chain 'm' and resid 161 through 166 Processing helix chain 'm' and resid 187 through 197 Processing helix chain 'm' and resid 217 through 229 Processing helix chain 'm' and resid 262 through 266 removed outlier: 3.658A pdb=" N ARG m 265 " --> pdb=" O PRO m 262 " (cutoff:3.500A) Processing helix chain 'm' and resid 269 through 285 Processing helix chain 'm' and resid 290 through 299 removed outlier: 3.808A pdb=" N GLU m 299 " --> pdb=" O LYS m 295 " (cutoff:3.500A) Processing helix chain 'm' and resid 333 through 337 Processing helix chain 'm' and resid 341 through 345 Processing helix chain 'm' and resid 347 through 357 Processing helix chain 'm' and resid 358 through 362 removed outlier: 3.558A pdb=" N ARG m 362 " --> pdb=" O TYR m 359 " (cutoff:3.500A) Processing helix chain 'm' and resid 373 through 377 Processing helix chain 'm' and resid 383 through 397 removed outlier: 3.804A pdb=" N TYR m 395 " --> pdb=" O SER m 391 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA m 397 " --> pdb=" O ASP m 393 " (cutoff:3.500A) Processing helix chain 'm' and resid 408 through 412 Processing helix chain 'm' and resid 418 through 422 Processing helix chain 'm' and resid 519 through 532 removed outlier: 3.948A pdb=" N ASN m 525 " --> pdb=" O ASP m 521 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS m 529 " --> pdb=" O ASN m 525 " (cutoff:3.500A) Processing helix chain 'm' and resid 533 through 538 removed outlier: 3.570A pdb=" N TYR m 536 " --> pdb=" O GLY m 533 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR m 538 " --> pdb=" O GLY m 535 " (cutoff:3.500A) Processing helix chain 'm' and resid 579 through 584 removed outlier: 3.747A pdb=" N GLU m 584 " --> pdb=" O GLN m 580 " (cutoff:3.500A) Processing helix chain 'm' and resid 616 through 619 removed outlier: 4.270A pdb=" N THR m 619 " --> pdb=" O SER m 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 616 through 619' Processing helix chain 'q' and resid 198 through 213 removed outlier: 3.687A pdb=" N THR q 202 " --> pdb=" O THR q 198 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL q 208 " --> pdb=" O MET q 204 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN q 213 " --> pdb=" O LYS q 209 " (cutoff:3.500A) Processing helix chain 'q' and resid 214 through 218 Processing helix chain 'q' and resid 226 through 239 removed outlier: 3.629A pdb=" N GLU q 237 " --> pdb=" O LYS q 233 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 252 removed outlier: 3.876A pdb=" N LEU q 252 " --> pdb=" O LYS q 248 " (cutoff:3.500A) Processing helix chain 'q' and resid 254 through 264 Processing helix chain 'q' and resid 281 through 293 Processing helix chain 'q' and resid 319 through 324 Processing helix chain 'q' and resid 331 through 342 removed outlier: 4.196A pdb=" N LEU q 336 " --> pdb=" O ALA q 332 " (cutoff:3.500A) Proline residue: q 337 - end of helix removed outlier: 3.600A pdb=" N LEU q 341 " --> pdb=" O PRO q 337 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP q 342 " --> pdb=" O VAL q 338 " (cutoff:3.500A) Processing helix chain 'q' and resid 357 through 368 Processing helix chain 'q' and resid 382 through 394 removed outlier: 3.858A pdb=" N LEU q 386 " --> pdb=" O ARG q 382 " (cutoff:3.500A) Processing helix chain 'q' and resid 404 through 408 Processing helix chain 'q' and resid 435 through 440 removed outlier: 3.808A pdb=" N SER q 439 " --> pdb=" O SER q 435 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG q 440 " --> pdb=" O VAL q 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 435 through 440' Processing helix chain 'q' and resid 443 through 462 Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 481 through 495 removed outlier: 4.444A pdb=" N ALA q 487 " --> pdb=" O GLU q 483 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL q 488 " --> pdb=" O GLU q 484 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE q 489 " --> pdb=" O ASP q 485 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU q 493 " --> pdb=" O ILE q 489 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS q 495 " --> pdb=" O TYR q 491 " (cutoff:3.500A) Processing helix chain 'q' and resid 515 through 519 removed outlier: 3.972A pdb=" N GLY q 518 " --> pdb=" O SER q 515 " (cutoff:3.500A) Processing helix chain 'q' and resid 522 through 528 Processing helix chain 'r' and resid 5 through 15 removed outlier: 3.589A pdb=" N ARG r 9 " --> pdb=" O ASP r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 19 through 30 removed outlier: 3.614A pdb=" N ARG r 23 " --> pdb=" O ASP r 19 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 42 removed outlier: 3.642A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 74 removed outlier: 4.047A pdb=" N LYS r 74 " --> pdb=" O GLN r 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 165 through 169 removed outlier: 3.861A pdb=" N GLU r 169 " --> pdb=" O VAL r 166 " (cutoff:3.500A) Processing helix chain 'r' and resid 206 through 213 Processing helix chain 's' and resid 12 through 36 removed outlier: 3.638A pdb=" N LYS s 35 " --> pdb=" O LYS s 31 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS s 36 " --> pdb=" O LYS s 32 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 52 through 59 Processing helix chain 'u' and resid 67 through 71 Processing helix chain 'u' and resid 82 through 112 removed outlier: 3.577A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 129 removed outlier: 3.519A pdb=" N LEU u 121 " --> pdb=" O GLU u 117 " (cutoff:3.500A) Processing helix chain 'u' and resid 130 through 140 removed outlier: 3.844A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU u 138 " --> pdb=" O LEU u 134 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL u 139 " --> pdb=" O ARG u 135 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU u 140 " --> pdb=" O ILE u 136 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 12 Processing helix chain 'v' and resid 33 through 40 Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 157 through 167 Processing helix chain 'v' and resid 178 through 193 Processing helix chain 'v' and resid 195 through 201 removed outlier: 3.630A pdb=" N PHE v 201 " --> pdb=" O LYS v 197 " (cutoff:3.500A) Processing helix chain 'v' and resid 211 through 227 Processing helix chain 'y' and resid 12 through 16 removed outlier: 3.574A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 12 through 16' Processing helix chain 'y' and resid 32 through 43 removed outlier: 3.617A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 107 Processing helix chain 'y' and resid 123 through 133 removed outlier: 3.743A pdb=" N GLU y 127 " --> pdb=" O ARG y 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU y 128 " --> pdb=" O GLU y 124 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.514A pdb=" N GLU y 172 " --> pdb=" O GLN y 168 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'z' and resid 7 through 19 Processing helix chain 'z' and resid 20 through 56 removed outlier: 4.000A pdb=" N VAL z 26 " --> pdb=" O PHE z 22 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU z 47 " --> pdb=" O LYS z 43 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY z 56 " --> pdb=" O LYS z 52 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 15 Processing helix chain '8' and resid 15 through 35 removed outlier: 4.164A pdb=" N GLY 8 35 " --> pdb=" O LYS 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 41 through 50 removed outlier: 3.916A pdb=" N ALA 8 48 " --> pdb=" O GLU 8 44 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 62 Processing helix chain '8' and resid 70 through 75 Processing helix chain '8' and resid 268 through 287 removed outlier: 3.602A pdb=" N LEU 8 281 " --> pdb=" O HIS 8 277 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU 8 282 " --> pdb=" O ALA 8 278 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE 8 283 " --> pdb=" O GLY 8 279 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN 8 286 " --> pdb=" O LEU 8 282 " (cutoff:3.500A) Processing helix chain '8' and resid 291 through 303 Processing helix chain '8' and resid 313 through 329 removed outlier: 3.582A pdb=" N GLU 8 317 " --> pdb=" O ARG 8 313 " (cutoff:3.500A) Processing helix chain '8' and resid 335 through 349 removed outlier: 3.842A pdb=" N PHE 8 339 " --> pdb=" O GLN 8 335 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE 8 343 " --> pdb=" O PHE 8 339 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN 8 344 " --> pdb=" O ALA 8 340 " (cutoff:3.500A) Processing helix chain '8' and resid 354 through 367 removed outlier: 3.761A pdb=" N LYS 8 367 " --> pdb=" O SER 8 363 " (cutoff:3.500A) Processing helix chain '8' and resid 376 through 392 Processing helix chain '8' and resid 396 through 420 removed outlier: 3.613A pdb=" N ARG 8 407 " --> pdb=" O PHE 8 403 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR 8 416 " --> pdb=" O HIS 8 412 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR 8 420 " --> pdb=" O THR 8 416 " (cutoff:3.500A) Processing helix chain '8' and resid 431 through 437 removed outlier: 3.806A pdb=" N ILE 8 435 " --> pdb=" O GLU 8 431 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 8 436 " --> pdb=" O ALA 8 432 " (cutoff:3.500A) Processing helix chain '8' and resid 438 through 456 removed outlier: 3.519A pdb=" N CYS 8 442 " --> pdb=" O ASN 8 438 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP 8 448 " --> pdb=" O SER 8 444 " (cutoff:3.500A) Processing helix chain '8' and resid 468 through 470 No H-bonds generated for 'chain '8' and resid 468 through 470' Processing helix chain '8' and resid 471 through 485 removed outlier: 3.526A pdb=" N GLY 8 481 " --> pdb=" O GLN 8 477 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE 8 483 " --> pdb=" O THR 8 479 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG 8 484 " --> pdb=" O LEU 8 480 " (cutoff:3.500A) Processing helix chain '8' and resid 491 through 510 Processing helix chain '8' and resid 515 through 525 removed outlier: 3.944A pdb=" N LEU 8 519 " --> pdb=" O ILE 8 515 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE 8 522 " --> pdb=" O LEU 8 518 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU 8 523 " --> pdb=" O LEU 8 519 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR 8 524 " --> pdb=" O SER 8 520 " (cutoff:3.500A) Processing helix chain '8' and resid 526 through 529 Processing helix chain '8' and resid 556 through 577 removed outlier: 3.602A pdb=" N GLU 8 565 " --> pdb=" O GLU 8 561 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL 8 568 " --> pdb=" O SER 8 564 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 8 570 " --> pdb=" O GLN 8 566 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE 8 575 " --> pdb=" O LEU 8 571 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU 8 577 " --> pdb=" O ASP 8 573 " (cutoff:3.500A) Processing helix chain '8' and resid 583 through 600 Proline residue: 8 590 - end of helix removed outlier: 3.512A pdb=" N LYS 8 600 " --> pdb=" O ARG 8 596 " (cutoff:3.500A) Processing helix chain '8' and resid 604 through 629 removed outlier: 3.999A pdb=" N ARG 8 610 " --> pdb=" O LYS 8 606 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU 8 616 " --> pdb=" O SER 8 612 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG 8 629 " --> pdb=" O ILE 8 625 " (cutoff:3.500A) Processing helix chain '8' and resid 640 through 645 removed outlier: 4.233A pdb=" N PHE 8 645 " --> pdb=" O GLU 8 641 " (cutoff:3.500A) Processing helix chain '8' and resid 654 through 678 removed outlier: 3.579A pdb=" N ARG 8 675 " --> pdb=" O ALA 8 671 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 151 removed outlier: 3.551A pdb=" N GLN I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 167 removed outlier: 3.598A pdb=" N GLU I 167 " --> pdb=" O CYS I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 181 removed outlier: 3.540A pdb=" N PHE I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 189 Processing helix chain 'I' and resid 198 through 203 removed outlier: 3.560A pdb=" N LYS I 202 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 236 Processing helix chain 'I' and resid 242 through 261 removed outlier: 3.673A pdb=" N SER I 261 " --> pdb=" O LYS I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 266 removed outlier: 4.174A pdb=" N HIS I 265 " --> pdb=" O THR I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 281 removed outlier: 3.758A pdb=" N ILE I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 305 removed outlier: 4.378A pdb=" N GLN I 293 " --> pdb=" O PRO I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 325 removed outlier: 3.642A pdb=" N GLU I 313 " --> pdb=" O SER I 309 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR I 324 " --> pdb=" O LYS I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 335 Processing helix chain 'I' and resid 336 through 344 removed outlier: 5.954A pdb=" N ASP I 341 " --> pdb=" O LEU I 338 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL I 342 " --> pdb=" O SER I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 366 removed outlier: 3.666A pdb=" N ARG I 366 " --> pdb=" O LYS I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 421 Processing helix chain 'I' and resid 425 through 436 Processing helix chain 'I' and resid 437 through 440 Processing helix chain 'I' and resid 444 through 463 removed outlier: 3.622A pdb=" N PHE I 461 " --> pdb=" O SER I 457 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP I 462 " --> pdb=" O ASP I 458 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN I 463 " --> pdb=" O THR I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 485 removed outlier: 4.095A pdb=" N ARG I 470 " --> pdb=" O SER I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 505 through 511 removed outlier: 3.637A pdb=" N LEU I 511 " --> pdb=" O PRO I 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 541 through 556 removed outlier: 3.678A pdb=" N PHE I 554 " --> pdb=" O LEU I 550 " (cutoff:3.500A) Processing helix chain 'I' and resid 561 through 577 Processing helix chain 'I' and resid 580 through 598 removed outlier: 3.647A pdb=" N ILE I 585 " --> pdb=" O GLU I 581 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA I 586 " --> pdb=" O LYS I 582 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN I 596 " --> pdb=" O ASP I 592 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG I 597 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 605 removed outlier: 3.615A pdb=" N LEU I 604 " --> pdb=" O ILE I 601 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 642 removed outlier: 3.728A pdb=" N ASN I 636 " --> pdb=" O LEU I 633 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU I 639 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU I 640 " --> pdb=" O ALA I 637 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS I 641 " --> pdb=" O LEU I 638 " (cutoff:3.500A) Processing helix chain 'I' and resid 644 through 662 removed outlier: 4.301A pdb=" N LYS I 659 " --> pdb=" O SER I 655 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU I 660 " --> pdb=" O SER I 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 49 removed outlier: 3.577A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 Processing helix chain 'K' and resid 107 through 114 removed outlier: 3.564A pdb=" N GLU K 112 " --> pdb=" O LYS K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 133 removed outlier: 3.798A pdb=" N ILE K 132 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS K 133 " --> pdb=" O SER K 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 129 through 133' Processing helix chain 'K' and resid 136 through 145 removed outlier: 3.791A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 157 through 163 removed outlier: 3.818A pdb=" N LYS K 161 " --> pdb=" O GLY K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 175 Processing helix chain 'K' and resid 185 through 188 removed outlier: 3.977A pdb=" N THR K 188 " --> pdb=" O SER K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 185 through 188' Processing helix chain 'K' and resid 189 through 194 removed outlier: 3.665A pdb=" N LEU K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 200 Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 255 through 274 removed outlier: 3.869A pdb=" N ASP K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 301 removed outlier: 3.621A pdb=" N GLU K 300 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 335 Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 128 through 133 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 20 No H-bonds generated for 'chain 'R' and resid 18 through 20' Processing helix chain 'R' and resid 28 through 33 Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 90 through 112 Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.599A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 153 removed outlier: 3.921A pdb=" N ILE R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA R 145 " --> pdb=" O HIS R 141 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 162 removed outlier: 3.708A pdb=" N ALA R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.542A pdb=" N LYS G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 95 removed outlier: 3.588A pdb=" N LEU G 93 " --> pdb=" O GLU G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 119 removed outlier: 3.703A pdb=" N GLU G 112 " --> pdb=" O ARG G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.681A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 182 through 190 removed outlier: 3.653A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 222 removed outlier: 3.504A pdb=" N ALA G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'G' and resid 239 through 245 removed outlier: 3.660A pdb=" N LYS G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 Processing helix chain 'Z' and resid 98 through 102 removed outlier: 3.527A pdb=" N PHE Z 101 " --> pdb=" O THR Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 123 Processing helix chain 'U' and resid 19 through 25 removed outlier: 3.719A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 39 removed outlier: 3.801A pdb=" N ILE U 38 " --> pdb=" O ALA U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 46 removed outlier: 3.800A pdb=" N GLY U 45 " --> pdb=" O LYS U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 Processing helix chain 'c' and resid 10 through 21 removed outlier: 3.503A pdb=" N LYS c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 36 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'g' and resid 58 through 65 removed outlier: 3.905A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR g 64 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL g 65 " --> pdb=" O TYR g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 Processing helix chain 'g' and resid 81 through 112 removed outlier: 3.726A pdb=" N ALA g 112 " --> pdb=" O GLN g 108 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 3.666A pdb=" N ARG k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 68 Processing helix chain 'n' and resid 10 through 15 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 64 through 73 removed outlier: 3.639A pdb=" N ILE n 68 " --> pdb=" O TYR n 64 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 96 removed outlier: 3.832A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 108 Processing helix chain 'n' and resid 114 through 122 Processing helix chain 'n' and resid 124 through 131 Processing helix chain 'n' and resid 132 through 143 Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 240 removed outlier: 3.594A pdb=" N THR n 220 " --> pdb=" O ARG n 216 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR n 234 " --> pdb=" O HIS n 230 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 254 removed outlier: 3.633A pdb=" N LYS n 254 " --> pdb=" O LEU n 250 " (cutoff:3.500A) Processing helix chain 'n' and resid 258 through 260 No H-bonds generated for 'chain 'n' and resid 258 through 260' Processing helix chain 'n' and resid 354 through 359 removed outlier: 3.708A pdb=" N LEU n 359 " --> pdb=" O VAL n 356 " (cutoff:3.500A) Processing helix chain 'n' and resid 372 through 383 removed outlier: 4.162A pdb=" N PHE n 378 " --> pdb=" O ASP n 374 " (cutoff:3.500A) Processing helix chain 'n' and resid 391 through 394 removed outlier: 3.788A pdb=" N ASP n 394 " --> pdb=" O ALA n 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 391 through 394' Processing helix chain 'n' and resid 429 through 439 removed outlier: 3.895A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) Processing helix chain 'n' and resid 443 through 448 removed outlier: 4.183A pdb=" N LYS n 446 " --> pdb=" O PRO n 443 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU n 448 " --> pdb=" O ASN n 445 " (cutoff:3.500A) Processing helix chain 'n' and resid 551 through 556 Processing helix chain 'n' and resid 557 through 559 No H-bonds generated for 'chain 'n' and resid 557 through 559' Processing helix chain 'n' and resid 560 through 594 removed outlier: 3.569A pdb=" N GLN n 594 " --> pdb=" O GLN n 590 " (cutoff:3.500A) Processing helix chain 'p' and resid 237 through 241 Processing helix chain 'p' and resid 247 through 252 removed outlier: 3.690A pdb=" N ASN p 252 " --> pdb=" O GLU p 248 " (cutoff:3.500A) Processing helix chain 'p' and resid 258 through 267 Processing helix chain 'p' and resid 268 through 270 No H-bonds generated for 'chain 'p' and resid 268 through 270' Processing helix chain 't' and resid 25 through 50 removed outlier: 3.902A pdb=" N LYS t 48 " --> pdb=" O GLN t 44 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 87 removed outlier: 3.522A pdb=" N ILE t 61 " --> pdb=" O ARG t 57 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 removed outlier: 3.752A pdb=" N ILE t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 183 through 188 removed outlier: 3.569A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) Processing helix chain 't' and resid 190 through 192 No H-bonds generated for 'chain 't' and resid 190 through 192' Processing helix chain 't' and resid 200 through 212 removed outlier: 3.659A pdb=" N LEU t 207 " --> pdb=" O SER t 203 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS t 210 " --> pdb=" O SER t 206 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG t 211 " --> pdb=" O LEU t 207 " (cutoff:3.500A) Processing helix chain 't' and resid 231 through 239 removed outlier: 4.183A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 246 through 256 removed outlier: 3.517A pdb=" N ILE t 250 " --> pdb=" O CYS t 246 " (cutoff:3.500A) Processing helix chain 't' and resid 260 through 266 Processing helix chain 't' and resid 281 through 294 Processing helix chain 't' and resid 313 through 322 removed outlier: 3.895A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 61 removed outlier: 3.700A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS D 59 " --> pdb=" O LYS D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.646A pdb=" N ARG D 71 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 79 removed outlier: 3.715A pdb=" N ALA D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.544A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Proline residue: D 99 - end of helix Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 123 through 137 removed outlier: 3.570A pdb=" N ALA D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.639A pdb=" N LYS D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 removed outlier: 3.528A pdb=" N LEU D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.588A pdb=" N GLY D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 removed outlier: 3.614A pdb=" N ARG D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.732A pdb=" N GLU D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 298 through 312 removed outlier: 3.681A pdb=" N TYR D 304 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 337 removed outlier: 3.508A pdb=" N ASN D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 removed outlier: 4.302A pdb=" N GLY D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 395 through 399 removed outlier: 3.858A pdb=" N LEU D 399 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 408 removed outlier: 4.264A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 422 removed outlier: 3.822A pdb=" N ILE D 422 " --> pdb=" O GLU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 436 through 456 Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.773A pdb=" N TYR D 477 " --> pdb=" O VAL D 473 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 142 through 153 removed outlier: 4.072A pdb=" N MET o 146 " --> pdb=" O LYS o 142 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE o 147 " --> pdb=" O GLU o 143 " (cutoff:3.500A) Processing helix chain 'o' and resid 192 through 211 removed outlier: 3.595A pdb=" N MET o 200 " --> pdb=" O LEU o 196 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS o 201 " --> pdb=" O LYS o 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU o 211 " --> pdb=" O ARG o 207 " (cutoff:3.500A) Processing helix chain 'o' and resid 212 through 214 No H-bonds generated for 'chain 'o' and resid 212 through 214' Processing helix chain 'w' and resid 259 through 265 Processing helix chain 'w' and resid 267 through 274 Processing helix chain 'w' and resid 284 through 292 removed outlier: 3.602A pdb=" N LYS w 292 " --> pdb=" O LYS w 288 " (cutoff:3.500A) Processing helix chain 'w' and resid 300 through 306 removed outlier: 3.836A pdb=" N ASP w 306 " --> pdb=" O SER w 302 " (cutoff:3.500A) Processing helix chain 'w' and resid 311 through 329 Processing helix chain 'w' and resid 348 through 388 removed outlier: 3.528A pdb=" N GLY w 358 " --> pdb=" O LYS w 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN w 375 " --> pdb=" O ARG w 371 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN w 388 " --> pdb=" O ARG w 384 " (cutoff:3.500A) Processing helix chain 'w' and resid 409 through 416 removed outlier: 3.656A pdb=" N THR w 416 " --> pdb=" O THR w 412 " (cutoff:3.500A) Processing helix chain 'w' and resid 419 through 425 Processing helix chain 'w' and resid 455 through 479 removed outlier: 3.957A pdb=" N ALA w 459 " --> pdb=" O SER w 455 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU w 463 " --> pdb=" O ALA w 459 " (cutoff:3.500A) Processing helix chain 'w' and resid 481 through 489 removed outlier: 3.812A pdb=" N ARG w 485 " --> pdb=" O ASP w 481 " (cutoff:3.500A) Processing helix chain 'w' and resid 552 through 559 removed outlier: 3.857A pdb=" N MET w 557 " --> pdb=" O SER w 553 " (cutoff:3.500A) Processing helix chain 'w' and resid 561 through 565 Processing helix chain 'w' and resid 620 through 625 Processing helix chain 'w' and resid 638 through 655 Processing helix chain 'w' and resid 659 through 671 removed outlier: 3.522A pdb=" N LEU w 665 " --> pdb=" O GLU w 661 " (cutoff:3.500A) Processing helix chain 'w' and resid 675 through 683 removed outlier: 3.587A pdb=" N VAL w 680 " --> pdb=" O LYS w 676 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP w 681 " --> pdb=" O HIS w 677 " (cutoff:3.500A) Processing helix chain 'w' and resid 696 through 706 removed outlier: 4.136A pdb=" N ASP w 702 " --> pdb=" O TRP w 698 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS w 706 " --> pdb=" O ASP w 702 " (cutoff:3.500A) Processing helix chain 'w' and resid 715 through 726 Processing helix chain 'w' and resid 732 through 758 Processing helix chain 'w' and resid 799 through 803 removed outlier: 3.572A pdb=" N LYS w 803 " --> pdb=" O GLY w 800 " (cutoff:3.500A) Processing helix chain 'w' and resid 820 through 837 removed outlier: 3.562A pdb=" N ASN w 825 " --> pdb=" O GLY w 821 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 17 Processing helix chain 'a' and resid 70 through 81 removed outlier: 3.658A pdb=" N ARG a 76 " --> pdb=" O PHE a 72 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS a 80 " --> pdb=" O ARG a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 92 removed outlier: 4.192A pdb=" N LYS a 92 " --> pdb=" O ASP a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 107 removed outlier: 4.010A pdb=" N TYR a 107 " --> pdb=" O LEU a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 124 Processing helix chain 'a' and resid 126 through 132 Processing helix chain 'a' and resid 144 through 153 removed outlier: 3.730A pdb=" N VAL a 148 " --> pdb=" O LEU a 144 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR a 149 " --> pdb=" O TYR a 145 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP a 150 " --> pdb=" O GLY a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 193 removed outlier: 3.622A pdb=" N PHE a 189 " --> pdb=" O MET a 185 " (cutoff:3.500A) Processing helix chain 'x' and resid 15 through 26 Processing helix chain 'x' and resid 31 through 42 removed outlier: 3.528A pdb=" N ILE x 38 " --> pdb=" O GLN x 34 " (cutoff:3.500A) Proline residue: x 39 - end of helix Processing helix chain 'x' and resid 56 through 72 Proline residue: x 64 - end of helix Processing helix chain 'x' and resid 92 through 108 Processing helix chain 'x' and resid 129 through 141 Processing helix chain 'x' and resid 148 through 158 Processing helix chain 'x' and resid 173 through 178 Processing helix chain 'x' and resid 182 through 193 removed outlier: 3.583A pdb=" N LYS x 188 " --> pdb=" O LYS x 184 " (cutoff:3.500A) Processing helix chain 'x' and resid 211 through 217 removed outlier: 3.701A pdb=" N PHE x 214 " --> pdb=" O SER x 211 " (cutoff:3.500A) Processing helix chain 'x' and resid 244 through 246 No H-bonds generated for 'chain 'x' and resid 244 through 246' Processing helix chain 'x' and resid 247 through 257 Processing helix chain 'x' and resid 270 through 287 Processing helix chain 'x' and resid 304 through 317 Processing helix chain 'x' and resid 353 through 358 Processing helix chain 'x' and resid 359 through 361 No H-bonds generated for 'chain 'x' and resid 359 through 361' Processing helix chain 'x' and resid 362 through 366 Processing helix chain 'x' and resid 378 through 389 removed outlier: 4.140A pdb=" N PHE x 382 " --> pdb=" O ARG x 378 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE x 383 " --> pdb=" O GLU x 379 " (cutoff:3.500A) Proline residue: x 384 - end of helix Processing helix chain 'x' and resid 406 through 416 Processing helix chain 'x' and resid 418 through 438 Processing helix chain 'x' and resid 451 through 459 Processing helix chain 'x' and resid 467 through 474 Processing helix chain 'x' and resid 502 through 515 removed outlier: 3.721A pdb=" N LYS x 507 " --> pdb=" O LYS x 503 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU x 508 " --> pdb=" O LYS x 504 " (cutoff:3.500A) Processing helix chain 'x' and resid 515 through 533 Processing helix chain 'x' and resid 536 through 558 removed outlier: 3.814A pdb=" N LYS x 556 " --> pdb=" O LYS x 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '7' and resid 12 through 15 removed outlier: 3.624A pdb=" N ARG N 71 " --> pdb=" O GLU 7 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '7' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain '7' and resid 89 through 90 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 89 through 90 current: chain 'A' and resid 59 through 61 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 61 current: chain 'A' and resid 96 through 102 removed outlier: 4.346A pdb=" N LEU A 97 " --> pdb=" O ILE A 114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 109 through 118 current: chain 'A' and resid 175 through 181 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 210 through 214 current: chain 'A' and resid 232 through 238 Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 42 through 43 current: chain 'B' and resid 100 through 106 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 100 through 106 current: chain 'B' and resid 178 through 184 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 60 removed outlier: 5.255A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 70 " --> pdb=" O LEU B 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 70 through 80 current: chain 'B' and resid 274 through 276 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 274 through 276 current: chain 'B' and resid 321 through 325 Processing sheet with id=AA6, first strand: chain 'C' and resid 15 through 21 removed outlier: 5.460A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 63 Processing sheet with id=AA8, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA9, first strand: chain 'E' and resid 77 through 80 removed outlier: 3.634A pdb=" N ARG E 77 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR E 62 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N HIS E 57 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR E 89 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE E 41 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR E 87 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.378A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL F 134 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB3, first strand: chain 'H' and resid 6 through 11 Processing sheet with id=AB4, first strand: chain 'H' and resid 17 through 21 Processing sheet with id=AB5, first strand: chain 'H' and resid 133 through 136 removed outlier: 6.220A pdb=" N ARG H 91 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL H 181 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL H 93 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE H 179 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 100 through 106 Processing sheet with id=AB7, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.442A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AB9, first strand: chain 'M' and resid 14 through 15 removed outlier: 3.588A pdb=" N PHE S 150 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 53 through 59 removed outlier: 5.036A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU M 68 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU M 22 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR M 66 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 36 through 38 removed outlier: 3.575A pdb=" N ASN N 122 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AC4, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AC5, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.776A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AC7, first strand: chain 'P' and resid 126 through 128 Processing sheet with id=AC8, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.323A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 56 through 64 removed outlier: 5.136A pdb=" N ILE S 58 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG S 12 " --> pdb=" O ILE S 58 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN T 149 " --> pdb=" O LEU S 24 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 87 through 96 removed outlier: 3.567A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 64 through 66 removed outlier: 7.217A pdb=" N VAL W 40 " --> pdb=" O TYR W 220 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR W 220 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL W 42 " --> pdb=" O SER W 218 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER W 218 " --> pdb=" O THR W 231 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR W 227 " --> pdb=" O ASP W 222 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 120 through 123 Processing sheet with id=AD4, first strand: chain 'W' and resid 135 through 137 removed outlier: 6.873A pdb=" N PHE W 135 " --> pdb=" O VAL W 188 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR W 186 " --> pdb=" O ILE W 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 174 through 176 Processing sheet with id=AD6, first strand: chain 'X' and resid 63 through 66 removed outlier: 3.966A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS X 109 " --> pdb=" O ARG X 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AD8, first strand: chain 'Y' and resid 81 through 82 removed outlier: 6.534A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AE1, first strand: chain 'b' and resid 169 through 172 removed outlier: 3.540A pdb=" N TYR b 205 " --> pdb=" O ASP b 220 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b' and resid 251 through 254 Processing sheet with id=AE3, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AE4, first strand: chain 'b' and resid 526 through 527 removed outlier: 6.525A pdb=" N LYS b 526 " --> pdb=" O THR U 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'd' and resid 49 through 51 removed outlier: 4.647A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 72 through 76 removed outlier: 5.941A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'f' and resid 8 through 18 removed outlier: 9.953A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.383A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AE9, first strand: chain 'l' and resid 2 through 3 removed outlier: 6.959A pdb=" N VAL l 44 " --> pdb=" O LEU l 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'l' and resid 63 through 66 removed outlier: 3.609A pdb=" N SER l 65 " --> pdb=" O VAL q 400 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'l' and resid 113 through 114 removed outlier: 6.892A pdb=" N VAL l 113 " --> pdb=" O VAL l 162 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE l 143 " --> pdb=" O GLN l 166 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP l 168 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU l 141 " --> pdb=" O ASP l 168 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA l 135 " --> pdb=" O PRO l 140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY l 142 " --> pdb=" O VAL l 133 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS l 96 " --> pdb=" O MET l 121 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N MET l 121 " --> pdb=" O LYS l 96 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP l 98 " --> pdb=" O GLY l 119 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'm' and resid 124 through 127 Processing sheet with id=AF4, first strand: chain 'm' and resid 170 through 173 removed outlier: 6.587A pdb=" N ILE m 180 " --> pdb=" O ILE m 171 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'm' and resid 202 through 206 removed outlier: 5.143A pdb=" N LEU m 205 " --> pdb=" O LEU m 214 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'm' and resid 399 through 405 Processing sheet with id=AF7, first strand: chain 'm' and resid 428 through 433 removed outlier: 6.839A pdb=" N LEU m 804 " --> pdb=" O SER m 430 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE m 432 " --> pdb=" O ALA m 802 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA m 802 " --> pdb=" O ILE m 432 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'm' and resid 442 through 445 removed outlier: 4.012A pdb=" N THR m 442 " --> pdb=" O GLY m 455 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL m 461 " --> pdb=" O ARG m 474 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG m 474 " --> pdb=" O VAL m 461 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL m 463 " --> pdb=" O VAL m 472 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'm' and resid 488 through 493 removed outlier: 6.815A pdb=" N ALA m 505 " --> pdb=" O GLU m 489 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE m 491 " --> pdb=" O ALA m 503 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA m 503 " --> pdb=" O ILE m 491 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE m 510 " --> pdb=" O THR m 590 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR m 590 " --> pdb=" O ILE m 510 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU m 512 " --> pdb=" O CYS m 588 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'm' and resid 599 through 602 removed outlier: 3.627A pdb=" N LYS m 599 " --> pdb=" O VAL m 612 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'm' and resid 642 through 647 removed outlier: 6.087A pdb=" N VAL m 662 " --> pdb=" O LYS m 675 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS m 675 " --> pdb=" O VAL m 662 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE m 664 " --> pdb=" O VAL m 673 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 683 through 688 removed outlier: 6.462A pdb=" N SER m 698 " --> pdb=" O SER m 684 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE m 686 " --> pdb=" O ILE m 696 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE m 696 " --> pdb=" O ILE m 686 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE m 688 " --> pdb=" O ASN m 694 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN m 694 " --> pdb=" O ILE m 688 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'm' and resid 726 through 731 removed outlier: 5.688A pdb=" N HIS m 751 " --> pdb=" O PRO m 766 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR m 753 " --> pdb=" O ILE m 764 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE m 764 " --> pdb=" O THR m 753 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'q' and resid 294 through 298 removed outlier: 3.662A pdb=" N ASP q 311 " --> pdb=" O ASN q 295 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLN q 297 " --> pdb=" O ILE q 309 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE q 309 " --> pdb=" O GLN q 297 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE q 271 " --> pdb=" O ILE q 309 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'q' and resid 417 through 420 Processing sheet with id=AG7, first strand: chain 'r' and resid 181 through 186 removed outlier: 3.713A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU r 222 " --> pdb=" O LEU r 198 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL r 200 " --> pdb=" O ILE r 220 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE r 220 " --> pdb=" O VAL r 200 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ALA r 257 " --> pdb=" O LYS r 181 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASN r 183 " --> pdb=" O ALA r 257 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU r 259 " --> pdb=" O ASN r 183 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR r 185 " --> pdb=" O LEU r 259 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AG9, first strand: chain 'u' and resid 28 through 30 Processing sheet with id=AH1, first strand: chain 'y' and resid 3 through 5 removed outlier: 6.799A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'y' and resid 17 through 19 Processing sheet with id=AH3, first strand: chain 'y' and resid 64 through 65 removed outlier: 6.324A pdb=" N LEU y 70 " --> pdb=" O GLN y 95 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AH5, first strand: chain 'y' and resid 152 through 154 Processing sheet with id=AH6, first strand: chain 'K' and resid 243 through 250 removed outlier: 6.380A pdb=" N LEU K 78 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ARG K 277 " --> pdb=" O TYR K 293 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR K 293 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 97 through 101 Processing sheet with id=AH8, first strand: chain 'K' and resid 153 through 156 removed outlier: 6.299A pdb=" N LEU K 124 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASP K 183 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE K 126 " --> pdb=" O ASP K 183 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 17 through 18 Processing sheet with id=AI1, first strand: chain 'V' and resid 22 through 25 removed outlier: 6.880A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 117 through 118 Processing sheet with id=AI3, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AI4, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AI5, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.358A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.675A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N HIS Z 40 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'U' and resid 54 through 58 removed outlier: 8.199A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N PHE U 107 " --> pdb=" O ASP U 18 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.055A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL c 67 " --> pdb=" O SER w 540 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.573A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'k' and resid 3 through 5 removed outlier: 4.378A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG k 46 " --> pdb=" O THR k 22 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA k 23 " --> pdb=" O ASN k 76 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'n' and resid 176 through 181 removed outlier: 6.799A pdb=" N GLN n 189 " --> pdb=" O ARG n 177 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL n 179 " --> pdb=" O TYR n 187 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR n 187 " --> pdb=" O VAL n 179 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'n' and resid 247 through 248 removed outlier: 4.236A pdb=" N LYS n 247 " --> pdb=" O ILE n 263 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE n 263 " --> pdb=" O LYS n 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'n' and resid 387 through 389 removed outlier: 6.334A pdb=" N GLN n 410 " --> pdb=" O ILE n 427 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'p' and resid 96 through 101 removed outlier: 3.741A pdb=" N ASN p 98 " --> pdb=" O ILE p 451 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'p' and resid 106 through 110 removed outlier: 6.320A pdb=" N GLY p 121 " --> pdb=" O SER p 107 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU p 109 " --> pdb=" O ILE p 119 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE p 119 " --> pdb=" O LEU p 109 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS p 138 " --> pdb=" O THR p 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 136 through 140 current: chain 'p' and resid 157 through 162 removed outlier: 6.193A pdb=" N LEU p 167 " --> pdb=" O ILE p 203 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE p 203 " --> pdb=" O LEU p 167 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU p 169 " --> pdb=" O LEU p 201 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS p 199 " --> pdb=" O LYS p 171 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ARG p 277 " --> pdb=" O LEU p 201 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE p 203 " --> pdb=" O ARG p 277 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'p' and resid 211 through 216 removed outlier: 3.650A pdb=" N SER p 281 " --> pdb=" O PHE p 233 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'p' and resid 290 through 293 removed outlier: 4.349A pdb=" N THR p 311 " --> pdb=" O SER p 307 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE p 312 " --> pdb=" O THR p 325 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR p 325 " --> pdb=" O ILE p 312 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR p 314 " --> pdb=" O ILE p 323 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'p' and resid 332 through 338 removed outlier: 4.225A pdb=" N HIS p 352 " --> pdb=" O SER p 348 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE p 353 " --> pdb=" O LEU p 371 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'p' and resid 378 through 383 removed outlier: 3.555A pdb=" N SER p 395 " --> pdb=" O THR p 399 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR p 399 " --> pdb=" O SER p 395 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR p 412 " --> pdb=" O VAL p 402 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP p 404 " --> pdb=" O PRO p 410 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 't' and resid 129 through 134 removed outlier: 3.503A pdb=" N THR t 104 " --> pdb=" O ILE t 129 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE t 99 " --> pdb=" O VAL t 309 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLU t 311 " --> pdb=" O PHE t 99 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU t 101 " --> pdb=" O GLU t 311 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 't' and resid 194 through 197 removed outlier: 3.865A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 't' and resid 213 through 216 Processing sheet with id=AK5, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.505A pdb=" N ILE D 117 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA D 170 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 119 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 118 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU D 193 " --> pdb=" O MET D 225 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'D' and resid 317 through 319 removed outlier: 6.172A pdb=" N LEU D 317 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N THR D 346 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU D 319 " --> pdb=" O THR D 346 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE D 292 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N CYS D 345 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL D 294 " --> pdb=" O CYS D 345 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE D 293 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE D 361 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE D 393 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLN D 363 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN D 413 " --> pdb=" O GLN D 266 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'o' and resid 117 through 124 removed outlier: 5.015A pdb=" N LEU o 117 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLU o 138 " --> pdb=" O LEU o 117 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU o 119 " --> pdb=" O PHE o 136 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE o 136 " --> pdb=" O GLU o 119 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ARG o 121 " --> pdb=" O TYR o 134 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR o 134 " --> pdb=" O ARG o 121 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA o 123 " --> pdb=" O ARG o 132 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR o 155 " --> pdb=" O LEU o 162 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'w' and resid 256 through 258 removed outlier: 6.455A pdb=" N THR w 257 " --> pdb=" O THR w 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK8 Processing sheet with id=AK9, first strand: chain 'w' and resid 794 through 797 removed outlier: 6.415A pdb=" N THR w 794 " --> pdb=" O LYS w 817 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL w 819 " --> pdb=" O THR w 794 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL w 796 " --> pdb=" O VAL w 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK9 Processing sheet with id=AL1, first strand: chain 'a' and resid 165 through 171 removed outlier: 5.803A pdb=" N ALA a 166 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL a 36 " --> pdb=" O ALA a 166 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA a 168 " --> pdb=" O LEU a 34 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU a 34 " --> pdb=" O ALA a 168 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY a 170 " --> pdb=" O VAL a 32 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN a 35 " --> pdb=" O VAL a 205 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'a' and resid 52 through 53 Processing sheet with id=AL3, first strand: chain 'a' and resid 66 through 68 Processing sheet with id=AL4, first strand: chain 'x' and resid 119 through 122 removed outlier: 6.162A pdb=" N GLN x 120 " --> pdb=" O ILE x 146 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER x 86 " --> pdb=" O LEU x 145 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLY x 147 " --> pdb=" O SER x 86 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE x 88 " --> pdb=" O GLY x 147 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU x 87 " --> pdb=" O VAL x 170 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASP x 172 " --> pdb=" O LEU x 87 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE x 89 " --> pdb=" O ASP x 172 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL x 47 " --> pdb=" O LEU x 201 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N SER x 203 " --> pdb=" O VAL x 47 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL x 49 " --> pdb=" O SER x 203 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP x 46 " --> pdb=" O VAL x 222 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE x 224 " --> pdb=" O ASP x 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL x 48 " --> pdb=" O ILE x 224 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'x' and resid 294 through 299 removed outlier: 6.364A pdb=" N LYS x 263 " --> pdb=" O LEU x 341 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE x 343 " --> pdb=" O LYS x 263 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE x 265 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N GLU x 394 " --> pdb=" O LEU x 236 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU x 238 " --> pdb=" O GLU x 394 " (cutoff:3.500A) 3895 hydrogen bonds defined for protein. 11160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2064 hydrogen bonds 3318 hydrogen bond angles 0 basepair planarities 830 basepair parallelities 1418 stacking parallelities Total time for adding SS restraints: 160.90 Time building geometry restraints manager: 61.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 24287 1.33 - 1.45: 54974 1.45 - 1.57: 76524 1.57 - 1.69: 5608 1.69 - 1.81: 446 Bond restraints: 161839 Sorted by residual: bond pdb=" N ASP m 710 " pdb=" CA ASP m 710 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.61e+00 bond pdb=" C3' G 1 644 " pdb=" O3' G 1 644 " ideal model delta sigma weight residual 1.417 1.441 -0.024 1.50e-02 4.44e+03 2.49e+00 bond pdb=" CA TYR Y 74 " pdb=" C TYR Y 74 " ideal model delta sigma weight residual 1.526 1.509 0.018 1.15e-02 7.56e+03 2.39e+00 bond pdb=" CB VAL w 819 " pdb=" CG1 VAL w 819 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 bond pdb=" O5' A 13376 " pdb=" C5' A 13376 " ideal model delta sigma weight residual 1.420 1.442 -0.022 1.50e-02 4.44e+03 2.08e+00 ... (remaining 161834 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.82: 16085 105.82 - 113.46: 95649 113.46 - 121.09: 76244 121.09 - 128.72: 40686 128.72 - 136.36: 3355 Bond angle restraints: 232019 Sorted by residual: angle pdb=" O3' G 1 644 " pdb=" C3' G 1 644 " pdb=" C2' G 1 644 " ideal model delta sigma weight residual 113.70 126.95 -13.25 1.50e+00 4.44e-01 7.81e+01 angle pdb=" O3' A 1 906 " pdb=" C3' A 1 906 " pdb=" C2' A 1 906 " ideal model delta sigma weight residual 113.70 124.49 -10.79 1.50e+00 4.44e-01 5.17e+01 angle pdb=" C4' G 1 908 " pdb=" C3' G 1 908 " pdb=" O3' G 1 908 " ideal model delta sigma weight residual 109.40 119.71 -10.31 1.50e+00 4.44e-01 4.73e+01 angle pdb=" C3' A 1 906 " pdb=" C2' A 1 906 " pdb=" O2' A 1 906 " ideal model delta sigma weight residual 110.70 120.71 -10.01 1.50e+00 4.44e-01 4.45e+01 angle pdb=" N PRO 8 306 " pdb=" CA PRO 8 306 " pdb=" CB PRO 8 306 " ideal model delta sigma weight residual 103.44 109.98 -6.54 1.12e+00 7.97e-01 3.41e+01 ... (remaining 232014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 94459 35.98 - 71.97: 6871 71.97 - 107.95: 739 107.95 - 143.94: 29 143.94 - 179.92: 47 Dihedral angle restraints: 102145 sinusoidal: 68203 harmonic: 33942 Sorted by residual: dihedral pdb=" C4' G 1 908 " pdb=" C3' G 1 908 " pdb=" C2' G 1 908 " pdb=" C1' G 1 908 " ideal model delta sinusoidal sigma weight residual -35.00 31.65 -66.65 1 8.00e+00 1.56e-02 9.06e+01 dihedral pdb=" C5' G 1 908 " pdb=" C4' G 1 908 " pdb=" C3' G 1 908 " pdb=" O3' G 1 908 " ideal model delta sinusoidal sigma weight residual 147.00 81.08 65.92 1 8.00e+00 1.56e-02 8.88e+01 dihedral pdb=" C4' C 1 484 " pdb=" C3' C 1 484 " pdb=" C2' C 1 484 " pdb=" C1' C 1 484 " ideal model delta sinusoidal sigma weight residual -35.00 29.90 -64.90 1 8.00e+00 1.56e-02 8.64e+01 ... (remaining 102142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 27164 0.090 - 0.181: 1105 0.181 - 0.271: 45 0.271 - 0.361: 1 0.361 - 0.452: 3 Chirality restraints: 28318 Sorted by residual: chirality pdb=" C3' A 1 906 " pdb=" C4' A 1 906 " pdb=" O3' A 1 906 " pdb=" C2' A 1 906 " both_signs ideal model delta sigma weight residual False -2.48 -2.03 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C3' G 1 644 " pdb=" C4' G 1 644 " pdb=" O3' G 1 644 " pdb=" C2' G 1 644 " both_signs ideal model delta sigma weight residual False -2.48 -2.03 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CA ASN K 338 " pdb=" N ASN K 338 " pdb=" C ASN K 338 " pdb=" CB ASN K 338 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 28315 not shown) Planarity restraints: 18974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 39 " -0.052 2.00e-02 2.50e+03 2.15e-02 1.38e+01 pdb=" N9 G 2 39 " 0.049 2.00e-02 2.50e+03 pdb=" C8 G 2 39 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G 2 39 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 2 39 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 2 39 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G 2 39 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G 2 39 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G 2 39 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 2 39 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 2 39 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G 2 39 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 88 " 0.034 2.00e-02 2.50e+03 1.56e-02 6.66e+00 pdb=" N9 A 2 88 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A 2 88 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A 2 88 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A 2 88 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A 2 88 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A 2 88 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A 2 88 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A 2 88 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A 2 88 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A 2 88 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 12933 " -0.033 2.00e-02 2.50e+03 1.52e-02 6.34e+00 pdb=" N9 A 12933 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A 12933 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A 12933 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A 12933 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A 12933 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A 12933 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A 12933 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 12933 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 12933 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 12933 " 0.005 2.00e-02 2.50e+03 ... (remaining 18971 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 3697 2.65 - 3.21: 130556 3.21 - 3.78: 265162 3.78 - 4.34: 374511 4.34 - 4.90: 540259 Nonbonded interactions: 1314185 Sorted by model distance: nonbonded pdb=" C5 C 1 890 " pdb=" NE ARG 8 37 " model vdw 2.090 3.420 nonbonded pdb=" N4 C 1 890 " pdb=" NH2 ARG 8 37 " model vdw 2.118 3.200 nonbonded pdb=" O2' U 11329 " pdb=" OP1 A 11330 " model vdw 2.193 2.440 nonbonded pdb=" OP2 U 11721 " pdb=" OH TYR R 124 " model vdw 2.197 2.440 nonbonded pdb=" O2' C 13194 " pdb=" O2 U 13195 " model vdw 2.198 2.440 ... (remaining 1314180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 max=1.00 mean=0.99 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: 4.740 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: 0.140 Extract box with map and model: 19.060 Check model and map are aligned: 1.440 Set scattering table: 0.920 Process input model: 455.390 Find NCS groups from input model: 3.880 Set up NCS constraints: 0.400 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:2.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 488.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 161839 Z= 0.180 Angle : 0.519 13.253 232019 Z= 0.276 Chirality : 0.037 0.452 28318 Planarity : 0.004 0.059 18974 Dihedral : 20.682 179.920 80095 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 0.12 % Allowed : 0.53 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.78 (0.08), residues: 11427 helix: -0.37 (0.07), residues: 4621 sheet: -0.02 (0.13), residues: 1560 loop : -0.67 (0.08), residues: 5246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP b 427 HIS 0.012 0.001 HIS D 457 PHE 0.024 0.001 PHE x 61 TYR 0.025 0.001 TYR S 172 ARG 0.009 0.000 ARG S 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1247 time to evaluate : 9.418 Fit side-chains revert: symmetry clash REVERT: A 240 LYS cc_start: 0.6649 (mmpt) cc_final: 0.6418 (mmmt) REVERT: H 151 VAL cc_start: 0.8286 (t) cc_final: 0.8046 (t) REVERT: N 124 ASP cc_start: 0.8028 (m-30) cc_final: 0.7736 (m-30) REVERT: b 339 LEU cc_start: 0.5617 (mt) cc_final: 0.5291 (mt) REVERT: e 81 ASP cc_start: 0.7903 (m-30) cc_final: 0.7698 (m-30) REVERT: h 102 GLU cc_start: 0.7577 (tp30) cc_final: 0.7230 (tp30) REVERT: l 33 LEU cc_start: 0.7825 (pp) cc_final: 0.7616 (mt) REVERT: l 151 SER cc_start: 0.8010 (p) cc_final: 0.7716 (m) REVERT: r 7 ILE cc_start: 0.8259 (mm) cc_final: 0.8001 (mm) REVERT: v 61 THR cc_start: 0.8493 (t) cc_final: 0.8289 (m) REVERT: 8 406 ILE cc_start: 0.5677 (pt) cc_final: 0.5459 (pt) REVERT: V 28 ASN cc_start: 0.7471 (p0) cc_final: 0.7218 (p0) REVERT: R 136 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.6232 (mtm110) REVERT: c 61 MET cc_start: 0.8128 (ttp) cc_final: 0.7915 (ttt) REVERT: p 170 TRP cc_start: 0.6373 (m100) cc_final: 0.5980 (m100) REVERT: x 280 PHE cc_start: 0.3289 (t80) cc_final: 0.2870 (t80) outliers start: 12 outliers final: 2 residues processed: 1255 average time/residue: 1.4044 time to fit residues: 3009.1850 Evaluate side-chains 926 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 923 time to evaluate : 9.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 435 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 1196 optimal weight: 6.9990 chunk 1074 optimal weight: 5.9990 chunk 595 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 724 optimal weight: 4.9990 chunk 573 optimal weight: 20.0000 chunk 1110 optimal weight: 6.9990 chunk 429 optimal weight: 10.0000 chunk 675 optimal weight: 6.9990 chunk 826 optimal weight: 6.9990 chunk 1286 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 22 GLN A 84 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS F 197 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN M 59 ASN N 178 HIS Q 45 ASN Q 73 GLN ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN W 44 HIS W 74 GLN W 88 ASN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 104 ASN f 106 ASN h 108 GLN l 117 HIS m 191 GLN m 566 ASN ** r 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 530 ASN I 642 HIS U 101 ASN c 36 GLN g 33 GLN n 445 ASN D 397 ASN D 441 GLN w 360 GLN w 386 GLN w 420 ASN a 57 ASN a 182 GLN x 9 ASN x 239 ASN x 244 ASN x 292 ASN ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 304 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 161839 Z= 0.409 Angle : 0.674 10.189 232019 Z= 0.348 Chirality : 0.045 0.298 28318 Planarity : 0.006 0.077 18974 Dihedral : 21.834 179.613 56353 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 1.05 % Allowed : 7.99 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.47 (0.08), residues: 11427 helix: 0.30 (0.07), residues: 4770 sheet: -0.06 (0.13), residues: 1537 loop : -0.89 (0.08), residues: 5120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP b 427 HIS 0.011 0.002 HIS y 50 PHE 0.035 0.002 PHE x 61 TYR 0.024 0.002 TYR S 172 ARG 0.010 0.001 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 960 time to evaluate : 9.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LYS cc_start: 0.6666 (mmpt) cc_final: 0.6415 (mmmt) REVERT: E 133 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6315 (mm-30) REVERT: Y 120 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8077 (mt0) REVERT: b 503 MET cc_start: 0.6255 (mtm) cc_final: 0.5925 (mtm) REVERT: b 519 MET cc_start: 0.6488 (tpt) cc_final: 0.6189 (tpt) REVERT: e 81 ASP cc_start: 0.7991 (m-30) cc_final: 0.7752 (m-30) REVERT: l 33 LEU cc_start: 0.8024 (pp) cc_final: 0.7658 (mt) REVERT: r 7 ILE cc_start: 0.8267 (mm) cc_final: 0.8000 (mm) REVERT: y 169 ASP cc_start: 0.5880 (m-30) cc_final: 0.5677 (m-30) REVERT: K 43 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6322 (tm-30) REVERT: V 12 ARG cc_start: 0.6537 (ttt90) cc_final: 0.6308 (ttt90) REVERT: V 28 ASN cc_start: 0.7567 (p0) cc_final: 0.7361 (p0) REVERT: V 54 LEU cc_start: 0.8715 (pt) cc_final: 0.8486 (pt) REVERT: Z 123 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: c 61 MET cc_start: 0.8255 (ttp) cc_final: 0.8033 (ttt) REVERT: o 217 GLU cc_start: 0.6717 (pp20) cc_final: 0.6312 (pp20) REVERT: w 363 GLN cc_start: 0.5886 (pp30) cc_final: 0.5643 (tt0) REVERT: a 174 MET cc_start: 0.2997 (mtp) cc_final: 0.2705 (mtt) REVERT: x 9 ASN cc_start: 0.0765 (OUTLIER) cc_final: 0.0256 (t0) REVERT: x 85 HIS cc_start: 0.7266 (t-90) cc_final: 0.6934 (t-90) REVERT: x 280 PHE cc_start: 0.3397 (t80) cc_final: 0.3011 (t80) REVERT: x 474 LEU cc_start: 0.5638 (tt) cc_final: 0.5436 (tt) outliers start: 106 outliers final: 73 residues processed: 1028 average time/residue: 1.3685 time to fit residues: 2426.3639 Evaluate side-chains 938 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 862 time to evaluate : 9.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 15 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 252 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain N residue 178 HIS Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 47 ASP Chi-restraints excluded: chain W residue 174 LYS Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 160 ILE Chi-restraints excluded: chain q residue 435 SER Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain r residue 245 VAL Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain v residue 43 SER Chi-restraints excluded: chain y residue 146 ILE Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 624 SER Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain V residue 29 SER Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain n residue 212 ASP Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 287 THR Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain w residue 317 MET Chi-restraints excluded: chain w residue 541 LYS Chi-restraints excluded: chain w residue 648 LYS Chi-restraints excluded: chain x residue 9 ASN Chi-restraints excluded: chain x residue 14 LEU Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 33 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 199 THR Chi-restraints excluded: chain x residue 213 ILE Chi-restraints excluded: chain x residue 313 THR Chi-restraints excluded: chain x residue 342 VAL Chi-restraints excluded: chain x residue 353 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 715 optimal weight: 0.8980 chunk 399 optimal weight: 9.9990 chunk 1070 optimal weight: 1.9990 chunk 876 optimal weight: 3.9990 chunk 354 optimal weight: 0.7980 chunk 1289 optimal weight: 0.5980 chunk 1392 optimal weight: 9.9990 chunk 1148 optimal weight: 5.9990 chunk 1278 optimal weight: 10.0000 chunk 439 optimal weight: 6.9990 chunk 1034 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 195 HIS ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN S 142 GLN W 44 HIS W 74 GLN W 88 ASN W 91 GLN b 454 GLN f 106 ASN m 550 ASN u 24 ASN ** u 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 462 ASN 8 621 ASN I 218 GLN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 GLN x 9 ASN x 250 GLN ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 161839 Z= 0.134 Angle : 0.500 8.843 232019 Z= 0.263 Chirality : 0.035 0.236 28318 Planarity : 0.004 0.053 18974 Dihedral : 21.747 179.521 56351 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 1.23 % Allowed : 9.54 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.08), residues: 11427 helix: 0.98 (0.08), residues: 4777 sheet: 0.05 (0.13), residues: 1540 loop : -0.72 (0.09), residues: 5110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 427 HIS 0.016 0.001 HIS N 178 PHE 0.024 0.001 PHE x 61 TYR 0.018 0.001 TYR b 91 ARG 0.004 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 971 time to evaluate : 9.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LYS cc_start: 0.6601 (mmpt) cc_final: 0.6355 (mmmt) REVERT: C 212 ASP cc_start: 0.8255 (t0) cc_final: 0.8047 (t70) REVERT: M 4 ASP cc_start: 0.7685 (m-30) cc_final: 0.7385 (t0) REVERT: P 180 LYS cc_start: 0.7365 (ttmt) cc_final: 0.7111 (tppt) REVERT: S 119 ARG cc_start: 0.7049 (ptp90) cc_final: 0.6811 (mtm-85) REVERT: Y 120 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: b 284 MET cc_start: 0.5736 (ttt) cc_final: 0.5496 (mtp) REVERT: b 531 MET cc_start: 0.5828 (tpt) cc_final: 0.5472 (tpt) REVERT: e 81 ASP cc_start: 0.7935 (m-30) cc_final: 0.7657 (m-30) REVERT: e 113 LYS cc_start: 0.8014 (tttm) cc_final: 0.7805 (ttpp) REVERT: i 54 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7632 (mm-30) REVERT: l 33 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7491 (mt) REVERT: q 237 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6539 (tt0) REVERT: r 13 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7472 (mm110) REVERT: I 458 ASP cc_start: 0.6535 (t0) cc_final: 0.6220 (m-30) REVERT: K 43 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6410 (tm-30) REVERT: K 326 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5907 (pp) REVERT: c 61 MET cc_start: 0.8209 (ttp) cc_final: 0.7983 (ttt) REVERT: n 229 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8037 (mm) REVERT: o 217 GLU cc_start: 0.6558 (pp20) cc_final: 0.6239 (pp20) REVERT: a 92 LYS cc_start: 0.4220 (pttp) cc_final: 0.3898 (ttpt) REVERT: a 174 MET cc_start: 0.2821 (mtp) cc_final: 0.2603 (mtt) REVERT: x 85 HIS cc_start: 0.7254 (t-90) cc_final: 0.6982 (t-90) REVERT: x 280 PHE cc_start: 0.3323 (t80) cc_final: 0.3073 (t80) outliers start: 124 outliers final: 70 residues processed: 1055 average time/residue: 1.3338 time to fit residues: 2449.3413 Evaluate side-chains 946 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 872 time to evaluate : 9.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 53 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 127 GLU Chi-restraints excluded: chain l residue 156 MET Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain m residue 135 ILE Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 521 ASP Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 150 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain v residue 43 SER Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 146 ILE Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 212 ASP Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 287 THR Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain w residue 568 GLU Chi-restraints excluded: chain x residue 33 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 266 VAL Chi-restraints excluded: chain x residue 342 VAL Chi-restraints excluded: chain x residue 353 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 1273 optimal weight: 10.0000 chunk 969 optimal weight: 5.9990 chunk 669 optimal weight: 0.0570 chunk 142 optimal weight: 10.0000 chunk 615 optimal weight: 7.9990 chunk 865 optimal weight: 1.9990 chunk 1293 optimal weight: 5.9990 chunk 1369 optimal weight: 20.0000 chunk 675 optimal weight: 6.9990 chunk 1226 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 GLN ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 HIS S 74 ASN S 142 GLN W 14 GLN W 44 HIS W 88 ASN b 26 GLN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 ASN m 550 ASN ** u 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 462 ASN 8 508 ASN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN w 363 GLN w 827 GLN x 34 GLN ** x 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 439 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 161839 Z= 0.290 Angle : 0.571 8.327 232019 Z= 0.297 Chirality : 0.040 0.279 28318 Planarity : 0.005 0.062 18974 Dihedral : 21.697 179.700 56351 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 1.74 % Allowed : 11.37 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.08), residues: 11427 helix: 0.99 (0.08), residues: 4789 sheet: -0.04 (0.13), residues: 1527 loop : -0.78 (0.09), residues: 5111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 427 HIS 0.008 0.001 HIS x 300 PHE 0.030 0.002 PHE x 61 TYR 0.023 0.002 TYR x 276 ARG 0.006 0.000 ARG O 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 887 time to evaluate : 8.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LYS cc_start: 0.6553 (mmpt) cc_final: 0.6316 (mmmt) REVERT: M 4 ASP cc_start: 0.7732 (m-30) cc_final: 0.7435 (t0) REVERT: P 180 LYS cc_start: 0.7342 (ttmt) cc_final: 0.7113 (tppt) REVERT: Q 69 ARG cc_start: 0.7057 (ttm170) cc_final: 0.6748 (mtt180) REVERT: S 57 GLU cc_start: 0.7812 (tt0) cc_final: 0.7287 (tt0) REVERT: S 119 ARG cc_start: 0.7053 (ptp90) cc_final: 0.6796 (mtm-85) REVERT: b 232 MET cc_start: 0.6149 (ptp) cc_final: 0.5897 (ptp) REVERT: b 284 MET cc_start: 0.5841 (ttt) cc_final: 0.5607 (mtp) REVERT: b 531 MET cc_start: 0.5692 (tpt) cc_final: 0.5176 (tpt) REVERT: e 81 ASP cc_start: 0.7992 (m-30) cc_final: 0.7743 (m-30) REVERT: h 102 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6995 (tp30) REVERT: l 33 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7516 (mt) REVERT: m 127 LYS cc_start: 0.6221 (tppp) cc_final: 0.5908 (mmtm) REVERT: q 342 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6963 (t0) REVERT: r 13 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7634 (mm110) REVERT: y 19 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6471 (pt) REVERT: K 326 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5813 (pp) REVERT: G 112 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6403 (mt-10) REVERT: Z 123 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: c 61 MET cc_start: 0.8192 (ttp) cc_final: 0.7933 (ttt) REVERT: n 229 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8237 (mm) REVERT: D 223 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6252 (pp30) REVERT: a 92 LYS cc_start: 0.4361 (pttp) cc_final: 0.3835 (ttpt) REVERT: a 174 MET cc_start: 0.3109 (mtp) cc_final: 0.2870 (mtt) REVERT: x 280 PHE cc_start: 0.3505 (t80) cc_final: 0.3139 (t80) outliers start: 175 outliers final: 124 residues processed: 1001 average time/residue: 1.3422 time to fit residues: 2339.2011 Evaluate side-chains 989 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 857 time to evaluate : 9.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 53 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 252 ASP Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 174 LYS Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 156 MET Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain m residue 135 ILE Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 547 LEU Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 342 ASP Chi-restraints excluded: chain q residue 435 SER Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 150 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 43 SER Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 146 ILE Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain 8 residue 374 MET Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 412 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 29 SER Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 212 ASP Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 234 TRP Chi-restraints excluded: chain p residue 287 THR Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain w residue 317 MET Chi-restraints excluded: chain w residue 389 MET Chi-restraints excluded: chain w residue 469 MET Chi-restraints excluded: chain w residue 568 GLU Chi-restraints excluded: chain w residue 754 ILE Chi-restraints excluded: chain w residue 819 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 33 VAL Chi-restraints excluded: chain x residue 46 ASP Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 213 ILE Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 266 VAL Chi-restraints excluded: chain x residue 342 VAL Chi-restraints excluded: chain x residue 353 MET Chi-restraints excluded: chain x residue 372 THR Chi-restraints excluded: chain x residue 374 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 1140 optimal weight: 3.9990 chunk 777 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 1019 optimal weight: 7.9990 chunk 565 optimal weight: 0.9990 chunk 1168 optimal weight: 3.9990 chunk 946 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 699 optimal weight: 4.9990 chunk 1229 optimal weight: 9.9990 chunk 345 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS F 80 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 GLN N 178 HIS Q 145 ASN S 142 GLN W 44 HIS b 26 GLN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN l 166 GLN m 550 ASN q 447 GLN u 101 GLN ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 462 ASN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 161839 Z= 0.273 Angle : 0.563 10.819 232019 Z= 0.293 Chirality : 0.040 0.276 28318 Planarity : 0.004 0.058 18974 Dihedral : 21.705 179.419 56351 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 2.12 % Allowed : 12.34 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.08), residues: 11427 helix: 1.02 (0.07), residues: 4792 sheet: -0.04 (0.13), residues: 1519 loop : -0.83 (0.09), residues: 5116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 427 HIS 0.008 0.001 HIS 8 18 PHE 0.028 0.002 PHE x 61 TYR 0.019 0.002 TYR b 91 ARG 0.005 0.000 ARG f 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 909 time to evaluate : 9.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 LYS cc_start: 0.6511 (mmpt) cc_final: 0.6304 (mmmt) REVERT: H 14 GLU cc_start: 0.7055 (pm20) cc_final: 0.6810 (pm20) REVERT: M 4 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7491 (t0) REVERT: P 180 LYS cc_start: 0.7449 (ttmt) cc_final: 0.7218 (tppt) REVERT: S 57 GLU cc_start: 0.8098 (tt0) cc_final: 0.7773 (tt0) REVERT: b 232 MET cc_start: 0.6172 (ptp) cc_final: 0.5911 (ptp) REVERT: b 284 MET cc_start: 0.5824 (ttt) cc_final: 0.5544 (mtp) REVERT: b 432 MET cc_start: 0.7802 (tpp) cc_final: 0.7263 (tpt) REVERT: e 81 ASP cc_start: 0.7945 (m-30) cc_final: 0.7705 (m-30) REVERT: h 8 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: l 33 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7457 (mt) REVERT: m 205 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8528 (pp) REVERT: r 13 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7468 (mm110) REVERT: y 19 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6433 (pt) REVERT: K 188 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7910 (p) REVERT: K 326 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5970 (pp) REVERT: V 28 ASN cc_start: 0.7574 (p0) cc_final: 0.7348 (p0) REVERT: G 112 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6400 (mt-10) REVERT: Z 123 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: c 61 MET cc_start: 0.8201 (ttp) cc_final: 0.7920 (ttt) REVERT: n 229 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8350 (mm) REVERT: D 223 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6276 (pp30) REVERT: w 827 GLN cc_start: 0.7967 (tp40) cc_final: 0.7434 (mm-40) REVERT: a 92 LYS cc_start: 0.4304 (pttp) cc_final: 0.3753 (ttpt) REVERT: a 174 MET cc_start: 0.3043 (mtp) cc_final: 0.2805 (mtt) REVERT: x 280 PHE cc_start: 0.3304 (t80) cc_final: 0.3026 (t80) outliers start: 213 outliers final: 146 residues processed: 1049 average time/residue: 1.3267 time to fit residues: 2437.2038 Evaluate side-chains 1019 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 862 time to evaluate : 9.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 53 GLU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 252 ASP Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 178 HIS Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 137 ILE Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 221 THR Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain h residue 8 GLU Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 127 GLU Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 156 MET Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain m residue 135 ILE Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 160 ILE Chi-restraints excluded: chain m residue 205 LEU Chi-restraints excluded: chain m residue 237 ILE Chi-restraints excluded: chain m residue 475 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 547 LEU Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 435 SER Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 150 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 43 SER Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 146 ILE Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 412 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 29 SER Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 212 ASP Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 234 TRP Chi-restraints excluded: chain p residue 287 THR Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain w residue 317 MET Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain w residue 568 GLU Chi-restraints excluded: chain w residue 688 THR Chi-restraints excluded: chain w residue 754 ILE Chi-restraints excluded: chain w residue 819 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 33 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 73 GLU Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 213 ILE Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 266 VAL Chi-restraints excluded: chain x residue 326 THR Chi-restraints excluded: chain x residue 342 VAL Chi-restraints excluded: chain x residue 353 MET Chi-restraints excluded: chain x residue 372 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 460 optimal weight: 4.9990 chunk 1233 optimal weight: 1.9990 chunk 270 optimal weight: 10.0000 chunk 804 optimal weight: 0.9990 chunk 338 optimal weight: 4.9990 chunk 1371 optimal weight: 30.0000 chunk 1138 optimal weight: 1.9990 chunk 634 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 453 optimal weight: 2.9990 chunk 719 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 GLN ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN W 44 HIS b 26 GLN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN m 550 ASN q 447 GLN ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN g 18 ASN ** x 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 161839 Z= 0.167 Angle : 0.506 10.225 232019 Z= 0.265 Chirality : 0.036 0.254 28318 Planarity : 0.004 0.058 18974 Dihedral : 21.667 179.163 56351 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.00 % Favored : 95.97 % Rotamer: Outliers : 1.82 % Allowed : 13.02 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.30 (0.08), residues: 11427 helix: 1.28 (0.08), residues: 4782 sheet: 0.00 (0.13), residues: 1520 loop : -0.74 (0.09), residues: 5125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 427 HIS 0.023 0.001 HIS N 178 PHE 0.024 0.001 PHE x 61 TYR 0.018 0.001 TYR y 113 ARG 0.004 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 918 time to evaluate : 9.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 196 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6548 (tpt170) REVERT: C 212 ASP cc_start: 0.8496 (t0) cc_final: 0.8208 (t70) REVERT: M 4 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7543 (t0) REVERT: N 124 ASP cc_start: 0.8024 (m-30) cc_final: 0.7730 (m-30) REVERT: P 180 LYS cc_start: 0.7416 (ttmt) cc_final: 0.7205 (tppt) REVERT: Q 24 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8728 (m) REVERT: S 57 GLU cc_start: 0.8095 (tt0) cc_final: 0.7787 (tt0) REVERT: S 157 GLN cc_start: 0.7565 (mt0) cc_final: 0.7289 (mt0) REVERT: W 221 TYR cc_start: 0.6551 (t80) cc_final: 0.6344 (t80) REVERT: b 232 MET cc_start: 0.5937 (ptp) cc_final: 0.5702 (ptp) REVERT: b 284 MET cc_start: 0.5715 (ttt) cc_final: 0.5445 (mtp) REVERT: b 432 MET cc_start: 0.7781 (tpp) cc_final: 0.7175 (tpt) REVERT: b 503 MET cc_start: 0.6402 (mtm) cc_final: 0.5959 (mtm) REVERT: e 81 ASP cc_start: 0.7976 (m-30) cc_final: 0.7724 (m-30) REVERT: e 113 LYS cc_start: 0.8039 (tttm) cc_final: 0.7823 (ttpp) REVERT: h 8 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: l 33 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7551 (mt) REVERT: q 259 MET cc_start: 0.4912 (tpp) cc_final: 0.4688 (tpt) REVERT: r 13 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7617 (mm110) REVERT: y 19 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6304 (pt) REVERT: 8 557 LYS cc_start: 0.6342 (mmmt) cc_final: 0.6059 (pttm) REVERT: K 188 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7878 (p) REVERT: K 326 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.6014 (pp) REVERT: R 136 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.5826 (mmm160) REVERT: G 112 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6413 (mt-10) REVERT: Z 123 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: U 38 ILE cc_start: 0.5804 (OUTLIER) cc_final: 0.5451 (pt) REVERT: c 61 MET cc_start: 0.8172 (ttp) cc_final: 0.7876 (ttt) REVERT: n 92 ARG cc_start: 0.8006 (ttt-90) cc_final: 0.7751 (ttp-170) REVERT: n 229 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8236 (mm) REVERT: t 144 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8640 (mt) REVERT: D 223 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6291 (pp30) REVERT: w 827 GLN cc_start: 0.7940 (tp40) cc_final: 0.7391 (mm-40) REVERT: a 92 LYS cc_start: 0.4225 (pttp) cc_final: 0.3736 (ttpt) REVERT: a 174 MET cc_start: 0.3001 (mtp) cc_final: 0.2774 (mtt) outliers start: 183 outliers final: 128 residues processed: 1039 average time/residue: 1.3208 time to fit residues: 2386.4913 Evaluate side-chains 1021 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 878 time to evaluate : 9.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 53 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain J residue 252 ASP Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain P residue 96 GLN Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain W residue 137 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain h residue 8 GLU Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 145 VAL Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 156 MET Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain m residue 135 ILE Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 475 THR Chi-restraints excluded: chain m residue 517 ILE Chi-restraints excluded: chain m residue 547 LEU Chi-restraints excluded: chain q residue 435 SER Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 150 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 43 SER Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 146 ILE Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 193 VAL Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 412 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain V residue 29 SER Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 212 ASP Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 417 LEU Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain n residue 589 LYS Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 234 TRP Chi-restraints excluded: chain p residue 287 THR Chi-restraints excluded: chain p residue 436 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 144 ILE Chi-restraints excluded: chain t residue 182 ASN Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain w residue 469 MET Chi-restraints excluded: chain w residue 568 GLU Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 819 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 33 VAL Chi-restraints excluded: chain x residue 40 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 185 ASP Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 326 THR Chi-restraints excluded: chain x residue 342 VAL Chi-restraints excluded: chain x residue 353 MET Chi-restraints excluded: chain x residue 374 LEU Chi-restraints excluded: chain x residue 394 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 1321 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 781 optimal weight: 8.9990 chunk 1001 optimal weight: 4.9990 chunk 775 optimal weight: 4.9990 chunk 1154 optimal weight: 10.0000 chunk 765 optimal weight: 3.9990 chunk 1365 optimal weight: 7.9990 chunk 854 optimal weight: 0.0980 chunk 832 optimal weight: 4.9990 chunk 630 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 GLN N 178 HIS S 142 GLN W 44 HIS b 26 GLN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 550 ASN ** u 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN g 18 ASN w 363 GLN w 549 HIS ** x 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 161839 Z= 0.220 Angle : 0.530 10.233 232019 Z= 0.277 Chirality : 0.038 0.265 28318 Planarity : 0.004 0.056 18974 Dihedral : 21.638 179.051 56351 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 2.17 % Allowed : 13.19 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.27 (0.08), residues: 11427 helix: 1.28 (0.08), residues: 4781 sheet: -0.03 (0.13), residues: 1504 loop : -0.78 (0.09), residues: 5142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 427 HIS 0.007 0.001 HIS 8 18 PHE 0.038 0.001 PHE x 280 TYR 0.020 0.001 TYR y 113 ARG 0.007 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 903 time to evaluate : 9.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7329 (tmm-80) REVERT: M 4 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7572 (t0) REVERT: N 124 ASP cc_start: 0.8052 (m-30) cc_final: 0.7783 (m-30) REVERT: P 180 LYS cc_start: 0.7429 (ttmt) cc_final: 0.7195 (tppt) REVERT: Q 24 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8767 (m) REVERT: S 57 GLU cc_start: 0.8120 (tt0) cc_final: 0.7856 (tt0) REVERT: S 157 GLN cc_start: 0.7582 (mt0) cc_final: 0.7309 (mt0) REVERT: W 67 MET cc_start: 0.6958 (mtp) cc_final: 0.6427 (mtp) REVERT: W 107 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6380 (tm-30) REVERT: W 221 TYR cc_start: 0.6589 (t80) cc_final: 0.6363 (t80) REVERT: b 232 MET cc_start: 0.5996 (ptp) cc_final: 0.5734 (ptp) REVERT: b 284 MET cc_start: 0.5684 (ttt) cc_final: 0.5428 (mtp) REVERT: b 432 MET cc_start: 0.7819 (tpp) cc_final: 0.7227 (tpt) REVERT: e 9 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8691 (mm) REVERT: e 81 ASP cc_start: 0.7951 (m-30) cc_final: 0.7705 (m-30) REVERT: e 113 LYS cc_start: 0.8076 (tttm) cc_final: 0.7846 (ttpp) REVERT: h 8 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: l 33 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7551 (mt) REVERT: v 55 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8490 (mt) REVERT: y 19 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6302 (pt) REVERT: z 49 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.4989 (mp) REVERT: 8 557 LYS cc_start: 0.6419 (mmmt) cc_final: 0.6083 (pttm) REVERT: K 188 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7894 (p) REVERT: K 326 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6127 (pp) REVERT: G 112 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6403 (mt-10) REVERT: Z 123 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: c 61 MET cc_start: 0.8217 (ttp) cc_final: 0.7877 (ttt) REVERT: n 92 ARG cc_start: 0.7985 (ttt-90) cc_final: 0.7737 (ttp-170) REVERT: n 229 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8334 (mm) REVERT: t 144 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8614 (mt) REVERT: D 108 LYS cc_start: 0.6262 (mmmt) cc_final: 0.6046 (tptt) REVERT: D 136 GLU cc_start: 0.7202 (tp30) cc_final: 0.6826 (tt0) REVERT: D 223 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6329 (pp30) REVERT: w 359 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5531 (tp) REVERT: w 827 GLN cc_start: 0.7967 (tp40) cc_final: 0.7424 (mm-40) REVERT: a 92 LYS cc_start: 0.4357 (pttp) cc_final: 0.3630 (ttpt) REVERT: a 174 MET cc_start: 0.3001 (mtp) cc_final: 0.2774 (mtt) outliers start: 218 outliers final: 165 residues processed: 1059 average time/residue: 1.3300 time to fit residues: 2460.4532 Evaluate side-chains 1058 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 875 time to evaluate : 9.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 53 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 252 ASP Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 96 GLN Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 9 ILE Chi-restraints excluded: chain h residue 8 GLU Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 156 MET Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain m residue 135 ILE Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 237 ILE Chi-restraints excluded: chain m residue 475 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 517 ILE Chi-restraints excluded: chain m residue 547 LEU Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 435 SER Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 150 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 43 SER Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 146 ILE Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 193 VAL Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain z residue 49 LEU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 412 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain I residue 592 ASP Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain V residue 12 ARG Chi-restraints excluded: chain V residue 29 SER Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 133 SER Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 212 ASP Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 417 LEU Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 234 TRP Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 287 THR Chi-restraints excluded: chain p residue 341 LEU Chi-restraints excluded: chain p residue 436 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 144 ILE Chi-restraints excluded: chain t residue 182 ASN Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain w residue 469 MET Chi-restraints excluded: chain w residue 568 GLU Chi-restraints excluded: chain w residue 688 THR Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 754 ILE Chi-restraints excluded: chain w residue 813 LYS Chi-restraints excluded: chain w residue 819 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 33 VAL Chi-restraints excluded: chain x residue 40 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 185 ASP Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 313 THR Chi-restraints excluded: chain x residue 326 THR Chi-restraints excluded: chain x residue 342 VAL Chi-restraints excluded: chain x residue 353 MET Chi-restraints excluded: chain x residue 372 THR Chi-restraints excluded: chain x residue 374 LEU Chi-restraints excluded: chain x residue 394 GLU Chi-restraints excluded: chain x residue 442 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 844 optimal weight: 5.9990 chunk 545 optimal weight: 0.9980 chunk 815 optimal weight: 1.9990 chunk 411 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 868 optimal weight: 3.9990 chunk 930 optimal weight: 30.0000 chunk 675 optimal weight: 0.2980 chunk 127 optimal weight: 7.9990 chunk 1073 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 GLN S 142 GLN W 44 HIS b 26 GLN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN z 31 GLN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN G 59 GLN g 18 ASN ** x 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.150 161839 Z= 0.155 Angle : 0.502 10.122 232019 Z= 0.264 Chirality : 0.036 0.275 28318 Planarity : 0.004 0.057 18974 Dihedral : 21.645 179.177 56351 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.08), residues: 11427 helix: 1.39 (0.08), residues: 4791 sheet: -0.00 (0.13), residues: 1533 loop : -0.73 (0.09), residues: 5103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 427 HIS 0.008 0.001 HIS q 469 PHE 0.026 0.001 PHE x 280 TYR 0.023 0.001 TYR y 113 ARG 0.007 0.000 ARG G 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 906 time to evaluate : 9.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 196 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7302 (tmm-80) REVERT: B 320 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6950 (m-30) REVERT: H 14 GLU cc_start: 0.7078 (pm20) cc_final: 0.6727 (pm20) REVERT: M 4 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7578 (t0) REVERT: N 124 ASP cc_start: 0.7948 (m-30) cc_final: 0.7671 (m-30) REVERT: P 180 LYS cc_start: 0.7426 (ttmt) cc_final: 0.7181 (tppt) REVERT: S 57 GLU cc_start: 0.8120 (tt0) cc_final: 0.7858 (tt0) REVERT: S 157 GLN cc_start: 0.7558 (mt0) cc_final: 0.7289 (mt0) REVERT: W 107 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6360 (tm-30) REVERT: W 221 TYR cc_start: 0.6236 (t80) cc_final: 0.5971 (t80) REVERT: b 284 MET cc_start: 0.5640 (ttt) cc_final: 0.5384 (mtp) REVERT: e 9 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8659 (mm) REVERT: e 81 ASP cc_start: 0.7901 (m-30) cc_final: 0.7661 (m-30) REVERT: e 113 LYS cc_start: 0.8012 (tttm) cc_final: 0.7802 (ttpp) REVERT: h 8 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: l 33 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7546 (mt) REVERT: v 55 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8468 (mt) REVERT: y 19 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6281 (pt) REVERT: z 49 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.4980 (mp) REVERT: 8 557 LYS cc_start: 0.6384 (mmmt) cc_final: 0.6055 (pttm) REVERT: K 188 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7860 (p) REVERT: K 326 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6087 (pp) REVERT: V 106 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8267 (tttt) REVERT: G 112 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: Z 123 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: c 61 MET cc_start: 0.8206 (ttp) cc_final: 0.7863 (ttt) REVERT: n 92 ARG cc_start: 0.7972 (ttt-90) cc_final: 0.7710 (ttp-170) REVERT: n 229 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8284 (mm) REVERT: t 144 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8640 (mt) REVERT: D 136 GLU cc_start: 0.7173 (tp30) cc_final: 0.6821 (tt0) REVERT: D 223 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6313 (pp30) REVERT: o 137 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7774 (pp) REVERT: w 359 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5531 (tp) REVERT: w 827 GLN cc_start: 0.7952 (tp40) cc_final: 0.7402 (mm-40) REVERT: a 92 LYS cc_start: 0.4308 (pttp) cc_final: 0.3613 (ttpt) REVERT: a 174 MET cc_start: 0.2960 (mtp) cc_final: 0.2734 (mtt) outliers start: 197 outliers final: 154 residues processed: 1044 average time/residue: 1.3307 time to fit residues: 2429.5908 Evaluate side-chains 1056 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 883 time to evaluate : 9.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 53 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 252 ASP Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain P residue 96 GLN Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 9 ILE Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain h residue 8 GLU Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 156 MET Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain m residue 135 ILE Chi-restraints excluded: chain m residue 237 ILE Chi-restraints excluded: chain m residue 475 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 517 ILE Chi-restraints excluded: chain m residue 521 ASP Chi-restraints excluded: chain m residue 547 LEU Chi-restraints excluded: chain m residue 770 LEU Chi-restraints excluded: chain q residue 267 ILE Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 150 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 43 SER Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 146 ILE Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain z residue 49 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 412 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain I residue 592 ASP Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 133 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain g residue 18 ASN Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 212 ASP Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 417 LEU Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 234 TRP Chi-restraints excluded: chain p residue 287 THR Chi-restraints excluded: chain p residue 341 LEU Chi-restraints excluded: chain p residue 436 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 144 ILE Chi-restraints excluded: chain t residue 182 ASN Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 137 LEU Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 208 ILE Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain w residue 469 MET Chi-restraints excluded: chain w residue 568 GLU Chi-restraints excluded: chain w residue 688 THR Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 754 ILE Chi-restraints excluded: chain w residue 813 LYS Chi-restraints excluded: chain w residue 819 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 33 VAL Chi-restraints excluded: chain x residue 40 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 185 ASP Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 342 VAL Chi-restraints excluded: chain x residue 353 MET Chi-restraints excluded: chain x residue 372 THR Chi-restraints excluded: chain x residue 374 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 1242 optimal weight: 9.9990 chunk 1308 optimal weight: 5.9990 chunk 1193 optimal weight: 5.9990 chunk 1272 optimal weight: 6.9990 chunk 766 optimal weight: 6.9990 chunk 554 optimal weight: 9.9990 chunk 999 optimal weight: 10.0000 chunk 390 optimal weight: 0.9990 chunk 1150 optimal weight: 8.9990 chunk 1203 optimal weight: 0.0870 chunk 1268 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 GLN N 178 HIS S 142 GLN W 44 HIS b 26 GLN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN m 123 ASN m 550 ASN z 31 GLN I 218 GLN K 294 ASN ** K 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN g 18 ASN ** x 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 161839 Z= 0.267 Angle : 0.557 10.032 232019 Z= 0.290 Chirality : 0.039 0.287 28318 Planarity : 0.004 0.070 18974 Dihedral : 21.627 178.980 56351 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.39 % Rotamer: Outliers : 2.19 % Allowed : 13.68 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.24 (0.08), residues: 11427 helix: 1.26 (0.08), residues: 4782 sheet: -0.08 (0.13), residues: 1507 loop : -0.79 (0.09), residues: 5138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 427 HIS 0.009 0.001 HIS x 300 PHE 0.034 0.002 PHE x 280 TYR 0.020 0.002 TYR y 113 ARG 0.006 0.000 ARG K 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 892 time to evaluate : 9.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7364 (tmm-80) REVERT: B 320 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: H 14 GLU cc_start: 0.7079 (pm20) cc_final: 0.6761 (pm20) REVERT: M 4 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7597 (t0) REVERT: N 124 ASP cc_start: 0.8092 (m-30) cc_final: 0.7777 (m-30) REVERT: P 180 LYS cc_start: 0.7445 (ttmt) cc_final: 0.7217 (tppt) REVERT: Q 24 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8770 (m) REVERT: S 57 GLU cc_start: 0.8139 (tt0) cc_final: 0.7925 (tt0) REVERT: S 157 GLN cc_start: 0.7589 (mt0) cc_final: 0.7320 (mt0) REVERT: W 67 MET cc_start: 0.6897 (mtp) cc_final: 0.6422 (mtp) REVERT: W 107 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: W 221 TYR cc_start: 0.6554 (t80) cc_final: 0.6347 (t80) REVERT: b 284 MET cc_start: 0.5809 (ttt) cc_final: 0.5548 (mtp) REVERT: e 9 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8693 (mm) REVERT: e 81 ASP cc_start: 0.7948 (m-30) cc_final: 0.7700 (m-30) REVERT: e 113 LYS cc_start: 0.8098 (tttm) cc_final: 0.7862 (ttpp) REVERT: h 8 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: l 33 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7509 (mt) REVERT: v 55 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8489 (mt) REVERT: y 19 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6384 (pt) REVERT: z 49 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.4989 (mp) REVERT: 8 557 LYS cc_start: 0.6251 (mmmt) cc_final: 0.5982 (pttm) REVERT: K 188 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7888 (p) REVERT: K 326 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5990 (pp) REVERT: V 106 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8276 (tttt) REVERT: G 112 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6398 (mt-10) REVERT: Z 123 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: c 61 MET cc_start: 0.8224 (ttp) cc_final: 0.7892 (ttt) REVERT: n 92 ARG cc_start: 0.7989 (ttt-90) cc_final: 0.7742 (ttp-170) REVERT: n 229 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8352 (mm) REVERT: t 144 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8635 (mt) REVERT: D 136 GLU cc_start: 0.7200 (tp30) cc_final: 0.6812 (tt0) REVERT: D 223 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6343 (pp30) REVERT: w 359 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5475 (tp) REVERT: w 827 GLN cc_start: 0.7987 (tp40) cc_final: 0.7451 (mm-40) REVERT: a 92 LYS cc_start: 0.4214 (pttp) cc_final: 0.3501 (ttpt) REVERT: a 174 MET cc_start: 0.2973 (mtp) cc_final: 0.2743 (mtt) outliers start: 221 outliers final: 174 residues processed: 1049 average time/residue: 1.3260 time to fit residues: 2426.0423 Evaluate side-chains 1067 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 874 time to evaluate : 9.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 53 GLU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 252 ASP Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 178 HIS Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 96 GLN Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 9 ILE Chi-restraints excluded: chain h residue 8 GLU Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 127 GLU Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 156 MET Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain m residue 123 ASN Chi-restraints excluded: chain m residue 135 ILE Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 160 ILE Chi-restraints excluded: chain m residue 237 ILE Chi-restraints excluded: chain m residue 475 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 517 ILE Chi-restraints excluded: chain m residue 547 LEU Chi-restraints excluded: chain m residue 771 THR Chi-restraints excluded: chain q residue 267 ILE Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 435 SER Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 150 MET Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 43 SER Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 146 ILE Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 193 VAL Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain z residue 49 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 412 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain I residue 592 ASP Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain V residue 12 ARG Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 133 SER Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain g residue 18 ASN Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 212 ASP Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 417 LEU Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 234 TRP Chi-restraints excluded: chain p residue 287 THR Chi-restraints excluded: chain p residue 341 LEU Chi-restraints excluded: chain p residue 436 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 144 ILE Chi-restraints excluded: chain t residue 182 ASN Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 208 ILE Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain w residue 469 MET Chi-restraints excluded: chain w residue 568 GLU Chi-restraints excluded: chain w residue 688 THR Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 754 ILE Chi-restraints excluded: chain w residue 813 LYS Chi-restraints excluded: chain w residue 819 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 33 VAL Chi-restraints excluded: chain x residue 40 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 185 ASP Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 313 THR Chi-restraints excluded: chain x residue 342 VAL Chi-restraints excluded: chain x residue 353 MET Chi-restraints excluded: chain x residue 372 THR Chi-restraints excluded: chain x residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 835 optimal weight: 10.0000 chunk 1345 optimal weight: 9.9990 chunk 821 optimal weight: 5.9990 chunk 638 optimal weight: 4.9990 chunk 935 optimal weight: 7.9990 chunk 1411 optimal weight: 5.9990 chunk 1299 optimal weight: 4.9990 chunk 1124 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 868 optimal weight: 7.9990 chunk 689 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 GLN ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN W 44 HIS b 26 GLN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 550 ASN z 31 GLN K 294 ASN K 295 GLN ** x 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 161839 Z= 0.298 Angle : 0.578 10.354 232019 Z= 0.300 Chirality : 0.040 0.283 28318 Planarity : 0.005 0.067 18974 Dihedral : 21.651 178.958 56351 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.32 % Rotamer: Outliers : 2.12 % Allowed : 13.84 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.08), residues: 11427 helix: 1.16 (0.08), residues: 4792 sheet: -0.14 (0.13), residues: 1537 loop : -0.83 (0.09), residues: 5098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 427 HIS 0.017 0.001 HIS N 178 PHE 0.038 0.002 PHE x 411 TYR 0.021 0.002 TYR y 113 ARG 0.008 0.000 ARG G 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22854 Ramachandran restraints generated. 11427 Oldfield, 0 Emsley, 11427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 885 time to evaluate : 9.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7365 (tmm-80) REVERT: B 320 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: M 4 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7619 (t0) REVERT: O 166 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: P 180 LYS cc_start: 0.7456 (ttmt) cc_final: 0.7234 (tppt) REVERT: Q 24 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8778 (m) REVERT: S 57 GLU cc_start: 0.8156 (tt0) cc_final: 0.7945 (tt0) REVERT: S 157 GLN cc_start: 0.7599 (mt0) cc_final: 0.7329 (mt0) REVERT: W 67 MET cc_start: 0.6920 (mtp) cc_final: 0.6494 (mtp) REVERT: W 107 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6361 (tm-30) REVERT: W 221 TYR cc_start: 0.6639 (t80) cc_final: 0.6436 (t80) REVERT: b 232 MET cc_start: 0.6103 (ptp) cc_final: 0.5821 (ptp) REVERT: b 284 MET cc_start: 0.5797 (ttt) cc_final: 0.5563 (mtp) REVERT: b 432 MET cc_start: 0.7836 (tpp) cc_final: 0.7253 (tpt) REVERT: e 9 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8739 (mm) REVERT: e 81 ASP cc_start: 0.7944 (m-30) cc_final: 0.7696 (m-30) REVERT: e 113 LYS cc_start: 0.8107 (tttm) cc_final: 0.7864 (ttpp) REVERT: h 8 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: l 33 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7537 (mt) REVERT: q 259 MET cc_start: 0.5337 (tpt) cc_final: 0.5002 (tpt) REVERT: v 55 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8495 (mt) REVERT: v 165 LEU cc_start: 0.6006 (tp) cc_final: 0.5782 (tp) REVERT: y 19 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6493 (pt) REVERT: z 49 LEU cc_start: 0.5384 (OUTLIER) cc_final: 0.4993 (mp) REVERT: K 188 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7900 (p) REVERT: G 112 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6407 (mt-10) REVERT: Z 123 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: c 61 MET cc_start: 0.8238 (ttp) cc_final: 0.7901 (ttt) REVERT: n 92 ARG cc_start: 0.7996 (ttt-90) cc_final: 0.7749 (ttp-170) REVERT: n 229 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8435 (mm) REVERT: t 144 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8622 (mt) REVERT: D 223 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6357 (pp30) REVERT: w 546 GLU cc_start: 0.5249 (mp0) cc_final: 0.4909 (mp0) REVERT: w 827 GLN cc_start: 0.7996 (tp40) cc_final: 0.7448 (mm-40) REVERT: a 92 LYS cc_start: 0.4250 (pttp) cc_final: 0.3481 (ttpt) REVERT: a 174 MET cc_start: 0.2932 (mtp) cc_final: 0.2704 (mtt) outliers start: 213 outliers final: 178 residues processed: 1033 average time/residue: 1.3454 time to fit residues: 2429.4658 Evaluate side-chains 1064 residues out of total 10147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 868 time to evaluate : 9.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 53 GLU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 252 ASP Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain L residue 62 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 96 GLN Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain S residue 8 GLN Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 107 GLU Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 178 VAL Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 315 VAL Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 9 ILE Chi-restraints excluded: chain h residue 4 VAL Chi-restraints excluded: chain h residue 8 GLU Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 127 GLU Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 156 MET Chi-restraints excluded: chain l residue 159 THR Chi-restraints excluded: chain m residue 135 ILE Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 160 ILE Chi-restraints excluded: chain m residue 237 ILE Chi-restraints excluded: chain m residue 475 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 517 ILE Chi-restraints excluded: chain m residue 547 LEU Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 771 THR Chi-restraints excluded: chain q residue 267 ILE Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 435 SER Chi-restraints excluded: chain r residue 65 ILE Chi-restraints excluded: chain r residue 71 SER Chi-restraints excluded: chain r residue 150 MET Chi-restraints excluded: chain r residue 245 VAL Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 43 SER Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain y residue 19 LEU Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 146 ILE Chi-restraints excluded: chain y residue 192 VAL Chi-restraints excluded: chain y residue 193 VAL Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain z residue 49 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 412 THR Chi-restraints excluded: chain I residue 588 LEU Chi-restraints excluded: chain I residue 592 ASP Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain V residue 12 ARG Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 133 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 136 ARG Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain n residue 8 THR Chi-restraints excluded: chain n residue 212 ASP Chi-restraints excluded: chain n residue 229 LEU Chi-restraints excluded: chain n residue 417 LEU Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain n residue 448 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 234 TRP Chi-restraints excluded: chain p residue 287 THR Chi-restraints excluded: chain p residue 341 LEU Chi-restraints excluded: chain p residue 436 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 144 ILE Chi-restraints excluded: chain t residue 182 ASN Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain o residue 95 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 208 ILE Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain w residue 469 MET Chi-restraints excluded: chain w residue 568 GLU Chi-restraints excluded: chain w residue 688 THR Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 754 ILE Chi-restraints excluded: chain w residue 813 LYS Chi-restraints excluded: chain w residue 819 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 33 VAL Chi-restraints excluded: chain x residue 40 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 73 GLU Chi-restraints excluded: chain x residue 125 THR Chi-restraints excluded: chain x residue 185 ASP Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 313 THR Chi-restraints excluded: chain x residue 326 THR Chi-restraints excluded: chain x residue 342 VAL Chi-restraints excluded: chain x residue 353 MET Chi-restraints excluded: chain x residue 372 THR Chi-restraints excluded: chain x residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1417 random chunks: chunk 892 optimal weight: 0.9990 chunk 1197 optimal weight: 0.9980 chunk 344 optimal weight: 8.9990 chunk 1036 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 1125 optimal weight: 4.9990 chunk 471 optimal weight: 8.9990 chunk 1156 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 GLN ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN W 44 HIS b 26 GLN ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 106 ASN m 123 ASN m 550 ASN z 31 GLN K 294 ASN g 18 ASN ** x 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.147392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126113 restraints weight = 212460.922| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.13 r_work: 0.3185 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 161839 Z= 0.200 Angle : 0.532 9.703 232019 Z= 0.279 Chirality : 0.038 0.290 28318 Planarity : 0.004 0.060 18974 Dihedral : 21.659 179.226 56351 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 2.02 % Allowed : 13.99 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.24 (0.08), residues: 11427 helix: 1.27 (0.08), residues: 4791 sheet: -0.09 (0.13), residues: 1525 loop : -0.80 (0.09), residues: 5111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 427 HIS 0.009 0.001 HIS x 300 PHE 0.038 0.001 PHE x 411 TYR 0.021 0.001 TYR y 113 ARG 0.007 0.000 ARG K 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37924.75 seconds wall clock time: 664 minutes 39.68 seconds (39879.68 seconds total)