Starting phenix.real_space_refine on Tue Feb 20 11:19:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plo_13494/02_2024/7plo_13494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plo_13494/02_2024/7plo_13494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plo_13494/02_2024/7plo_13494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plo_13494/02_2024/7plo_13494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plo_13494/02_2024/7plo_13494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plo_13494/02_2024/7plo_13494_updated.pdb" } resolution = 2.8 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7394 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 64 5.49 5 Mg 3 5.21 5 S 479 5.16 5 C 49658 2.51 5 N 13785 2.21 5 O 14857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 78855 Number of models: 1 Model: "" Number of chains: 35 Chain: "Q" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 683 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain breaks: 2 Chain: "2" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5527 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 29, 'TRANS': 667} Chain breaks: 2 Chain: "3" Number of atoms: 4908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4908 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 604} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4925 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 28, 'TRANS': 590} Chain breaks: 3 Chain: "5" Number of atoms: 4803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4803 Classifications: {'peptide': 614} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 587} Chain breaks: 2 Chain: "6" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5004 Classifications: {'peptide': 631} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "7" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4818 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 27, 'TRANS': 579} Chain breaks: 2 Chain: "A" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4195 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 487} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 6050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 6050 Classifications: {'peptide': 759} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 29, 'TRANS': 729} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4347 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 520} Chain breaks: 1 Chain: "D" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1613 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "E" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1431 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 163} Chain: "F" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1679 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "H" Number of atoms: 3178 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} Conformer: "B" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} bond proxies already assigned to first conformer: 3234 Chain: "I" Number of atoms: 3473 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3464 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 451, 3464 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 3536 Chain: "J" Number of atoms: 3183 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} Conformer: "B" Number of residues, atoms: 401, 3169 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 382} bond proxies already assigned to first conformer: 3228 Chain: "K" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5247 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 14, 'TRANS': 624} Chain breaks: 1 Chain: "L" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 726 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "M" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 682 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "N" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 438 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "O" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2888 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 366} Chain breaks: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "P" Number of atoms: 629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 82, 627 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 74} Chain breaks: 5 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 82, 627 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 74} Chain breaks: 5 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 631 Chain: "R" Number of atoms: 701 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 700 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 91, 700 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 711 Chain: "S" Number of atoms: 5386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5386 Classifications: {'peptide': 671} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 647} Chain breaks: 15 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "T" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 685 Classifications: {'peptide': 86} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1995 SG CYS 2 329 132.080 132.843 116.903 1.00 42.49 S ATOM 2018 SG CYS 2 332 135.173 132.499 115.152 1.00 62.06 S ATOM 2169 SG CYS 2 352 134.062 135.918 116.895 1.00 50.13 S ATOM 2191 SG CYS 2 355 132.885 134.696 113.364 1.00 72.73 S ATOM 12339 SG CYS 4 306 108.935 167.454 128.454 1.00 12.56 S ATOM 12361 SG CYS 4 309 108.895 171.243 128.736 1.00 22.48 S ATOM 12507 SG CYS 4 328 106.569 169.344 126.281 1.00 22.54 S ATOM 12528 SG CYS 4 331 110.212 169.596 125.543 1.00 23.44 S ATOM 17273 SG CYS 5 172 116.248 124.335 106.612 1.00 69.87 S ATOM 17296 SG CYS 5 175 117.370 124.176 103.255 1.00 73.71 S ATOM 17467 SG CYS 5 197 119.539 125.809 105.667 1.00 75.02 S ATOM 22110 SG CYS 6 158 124.618 158.650 126.607 1.00 19.94 S ATOM 22132 SG CYS 6 161 126.973 161.481 125.823 1.00 25.63 S ATOM 22293 SG CYS 6 180 123.541 162.159 127.123 1.00 24.22 S ATOM 22332 SG CYS 6 185 124.025 160.824 123.484 1.00 33.70 S ATOM 27254 SG CYS 7 184 84.943 155.544 112.652 1.00 16.08 S ATOM 27277 SG CYS 7 187 83.229 155.694 109.328 1.00 25.18 S ATOM 27423 SG CYS 7 206 85.794 152.834 110.254 1.00 19.14 S ATOM 27460 SG CYS 7 211 86.893 156.438 109.557 1.00 33.61 S ATOM 40438 SG CYS B2221 122.787 70.524 182.554 1.00 82.80 S ATOM 40461 SG CYS B2224 119.572 71.831 184.070 1.00 79.16 S ATOM 40554 SG CYS B2236 119.829 68.182 182.038 1.00 78.29 S ATOM 78274 SG CYS T 42 30.297 77.208 59.470 1.00122.13 S ATOM 78293 SG CYS T 45 31.999 80.125 60.026 1.00119.26 S ATOM 78513 SG CYS T 75 24.157 68.747 69.356 1.00119.70 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN H 810 " occ=0.53 ... (16 atoms not shown) pdb=" NE2BGLN H 810 " occ=0.47 residue: pdb=" N AGLN I 810 " occ=0.53 ... (16 atoms not shown) pdb=" NE2BGLN I 810 " occ=0.47 residue: pdb=" N AGLN J 810 " occ=0.53 ... (16 atoms not shown) pdb=" NE2BGLN J 810 " occ=0.47 Time building chain proxies: 35.18, per 1000 atoms: 0.45 Number of scatterers: 78855 At special positions: 0 Unit cell: (277.648, 239.056, 255.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 479 16.00 P 64 15.00 Mg 3 11.99 O 14857 8.00 N 13785 7.00 C 49658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B2158 " - pdb=" SG CYS B2161 " distance=2.03 Simple disulfide: pdb=" SG CYS B2158 " - pdb=" SG CYS B2190 " distance=2.04 Simple disulfide: pdb=" SG CYS B2161 " - pdb=" SG CYS B2187 " distance=2.05 Simple disulfide: pdb=" SG CYS B2161 " - pdb=" SG CYS B2190 " distance=2.05 Simple disulfide: pdb=" SG CYS B2187 " - pdb=" SG CYS B2190 " distance=2.02 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: 25.54 Conformation dependent library (CDL) restraints added in 12.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21001 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 329 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 355 " pdb=" ZN 4 901 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb=" ZN 5 802 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 5 802 " - pdb=" SG CYS 5 197 " pdb=" ZN 6 901 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 180 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 185 " pdb=" ZN 71000 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 211 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 206 " pdb=" ZN B2301 " pdb="ZN ZN B2301 " - pdb=" SG CYS B2224 " pdb="ZN ZN B2301 " - pdb=" SG CYS B2236 " pdb="ZN ZN B2301 " - pdb=" SG CYS B2221 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 42 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 45 " pdb="ZN ZN T 201 " - pdb=" ND1 HIS T 80 " pdb=" ZN T 203 " pdb="ZN ZN T 203 " - pdb=" SG CYS T 75 " Number of angles added : 24 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 384 helices and 87 sheets defined 42.4% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.00 Creating SS restraints... Processing helix chain 'Q' and resid 285 through 299 Processing helix chain 'Q' and resid 314 through 318 Processing helix chain 'Q' and resid 526 through 538 Processing helix chain 'Q' and resid 594 through 617 removed outlier: 4.037A pdb=" N ALA Q 604 " --> pdb=" O LYS Q 600 " (cutoff:3.500A) Processing helix chain '2' and resid 182 through 187 Processing helix chain '2' and resid 189 through 205 Processing helix chain '2' and resid 214 through 225 Processing helix chain '2' and resid 234 through 240 Processing helix chain '2' and resid 242 through 248 Processing helix chain '2' and resid 252 through 270 Processing helix chain '2' and resid 274 through 276 No H-bonds generated for 'chain '2' and resid 274 through 276' Processing helix chain '2' and resid 294 through 296 No H-bonds generated for 'chain '2' and resid 294 through 296' Processing helix chain '2' and resid 299 through 301 No H-bonds generated for 'chain '2' and resid 299 through 301' Processing helix chain '2' and resid 400 through 402 No H-bonds generated for 'chain '2' and resid 400 through 402' Processing helix chain '2' and resid 424 through 430 Processing helix chain '2' and resid 458 through 470 removed outlier: 3.621A pdb=" N LYS 2 469 " --> pdb=" O THR 2 465 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP 2 470 " --> pdb=" O SER 2 466 " (cutoff:3.500A) Processing helix chain '2' and resid 473 through 479 Processing helix chain '2' and resid 489 through 500 Processing helix chain '2' and resid 507 through 509 No H-bonds generated for 'chain '2' and resid 507 through 509' Processing helix chain '2' and resid 529 through 539 Processing helix chain '2' and resid 548 through 550 No H-bonds generated for 'chain '2' and resid 548 through 550' Processing helix chain '2' and resid 553 through 557 Processing helix chain '2' and resid 575 through 578 No H-bonds generated for 'chain '2' and resid 575 through 578' Processing helix chain '2' and resid 589 through 591 No H-bonds generated for 'chain '2' and resid 589 through 591' Processing helix chain '2' and resid 594 through 605 removed outlier: 3.949A pdb=" N SER 2 599 " --> pdb=" O GLN 2 595 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE 2 600 " --> pdb=" O ASP 2 596 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N HIS 2 601 " --> pdb=" O ARG 2 597 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU 2 602 " --> pdb=" O THR 2 598 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ALA 2 603 " --> pdb=" O SER 2 599 " (cutoff:3.500A) Processing helix chain '2' and resid 633 through 635 No H-bonds generated for 'chain '2' and resid 633 through 635' Processing helix chain '2' and resid 643 through 646 No H-bonds generated for 'chain '2' and resid 643 through 646' Processing helix chain '2' and resid 651 through 656 removed outlier: 3.710A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) Processing helix chain '2' and resid 669 through 685 Processing helix chain '2' and resid 717 through 729 Processing helix chain '2' and resid 740 through 756 removed outlier: 3.631A pdb=" N LYS 2 752 " --> pdb=" O SER 2 748 " (cutoff:3.500A) Processing helix chain '2' and resid 765 through 780 Processing helix chain '2' and resid 788 through 804 Processing helix chain '2' and resid 808 through 822 removed outlier: 4.599A pdb=" N ARG 2 812 " --> pdb=" O PHE 2 808 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER 2 813 " --> pdb=" O SER 2 809 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR 2 821 " --> pdb=" O THR 2 817 " (cutoff:3.500A) Processing helix chain '2' and resid 827 through 846 removed outlier: 4.000A pdb=" N GLU 2 830 " --> pdb=" O ASP 2 827 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE 2 835 " --> pdb=" O LEU 2 832 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU 2 842 " --> pdb=" O LEU 2 839 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN 2 843 " --> pdb=" O VAL 2 840 " (cutoff:3.500A) Processing helix chain '2' and resid 861 through 871 removed outlier: 3.577A pdb=" N GLN 2 871 " --> pdb=" O ASP 2 867 " (cutoff:3.500A) Processing helix chain '2' and resid 877 through 882 removed outlier: 3.624A pdb=" N TYR 2 881 " --> pdb=" O LEU 2 877 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP 2 882 " --> pdb=" O SER 2 878 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 877 through 882' Processing helix chain '2' and resid 884 through 888 Processing helix chain '3' and resid 9 through 23 Processing helix chain '3' and resid 31 through 41 Processing helix chain '3' and resid 51 through 57 Processing helix chain '3' and resid 59 through 67 Processing helix chain '3' and resid 69 through 87 Processing helix chain '3' and resid 91 through 93 No H-bonds generated for 'chain '3' and resid 91 through 93' Processing helix chain '3' and resid 107 through 109 No H-bonds generated for 'chain '3' and resid 107 through 109' Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 205 through 207 No H-bonds generated for 'chain '3' and resid 205 through 207' Processing helix chain '3' and resid 283 through 291 Processing helix chain '3' and resid 295 through 301 Processing helix chain '3' and resid 311 through 322 Processing helix chain '3' and resid 351 through 361 Processing helix chain '3' and resid 375 through 379 Processing helix chain '3' and resid 397 through 400 No H-bonds generated for 'chain '3' and resid 397 through 400' Processing helix chain '3' and resid 411 through 413 No H-bonds generated for 'chain '3' and resid 411 through 413' Processing helix chain '3' and resid 416 through 428 removed outlier: 4.571A pdb=" N ALA 3 421 " --> pdb=" O MET 3 417 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE 3 422 " --> pdb=" O ASP 3 418 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 465 through 468 No H-bonds generated for 'chain '3' and resid 465 through 468' Processing helix chain '3' and resid 473 through 478 removed outlier: 4.197A pdb=" N ARG 3 478 " --> pdb=" O SER 3 474 " (cutoff:3.500A) Processing helix chain '3' and resid 491 through 506 Processing helix chain '3' and resid 559 through 561 No H-bonds generated for 'chain '3' and resid 559 through 561' Processing helix chain '3' and resid 565 through 577 removed outlier: 3.580A pdb=" N LYS 3 570 " --> pdb=" O ALA 3 566 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE 3 577 " --> pdb=" O HIS 3 573 " (cutoff:3.500A) Processing helix chain '3' and resid 584 through 603 Processing helix chain '3' and resid 615 through 632 Processing helix chain '3' and resid 639 through 653 removed outlier: 3.535A pdb=" N GLU 3 644 " --> pdb=" O GLN 3 640 " (cutoff:3.500A) Processing helix chain '4' and resid 147 through 149 No H-bonds generated for 'chain '4' and resid 147 through 149' Processing helix chain '4' and resid 159 through 172 Processing helix chain '4' and resid 192 through 203 removed outlier: 3.648A pdb=" N ARG 4 196 " --> pdb=" O LEU 4 192 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 218 Processing helix chain '4' and resid 220 through 228 Processing helix chain '4' and resid 230 through 247 Proline residue: 4 235 - end of helix Processing helix chain '4' and resid 276 through 278 No H-bonds generated for 'chain '4' and resid 276 through 278' Processing helix chain '4' and resid 443 through 454 removed outlier: 4.239A pdb=" N LEU 4 448 " --> pdb=" O LYS 4 444 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU 4 451 " --> pdb=" O GLU 4 447 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG 4 454 " --> pdb=" O LYS 4 450 " (cutoff:3.500A) Processing helix chain '4' and resid 458 through 465 Processing helix chain '4' and resid 468 through 470 No H-bonds generated for 'chain '4' and resid 468 through 470' Processing helix chain '4' and resid 474 through 485 Processing helix chain '4' and resid 516 through 526 Processing helix chain '4' and resid 562 through 565 No H-bonds generated for 'chain '4' and resid 562 through 565' Processing helix chain '4' and resid 576 through 578 No H-bonds generated for 'chain '4' and resid 576 through 578' Processing helix chain '4' and resid 581 through 593 Processing helix chain '4' and resid 630 through 634 Processing helix chain '4' and resid 638 through 643 removed outlier: 3.754A pdb=" N ARG 4 643 " --> pdb=" O THR 4 639 " (cutoff:3.500A) Processing helix chain '4' and resid 656 through 670 removed outlier: 4.601A pdb=" N ARG 4 661 " --> pdb=" O ALA 4 657 " (cutoff:3.500A) Processing helix chain '4' and resid 674 through 697 removed outlier: 3.762A pdb=" N GLU 4 679 " --> pdb=" O GLU 4 675 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR 4 697 " --> pdb=" O TYR 4 693 " (cutoff:3.500A) Processing helix chain '4' and resid 704 through 722 removed outlier: 3.849A pdb=" N ILE 4 720 " --> pdb=" O ASP 4 716 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY 4 721 " --> pdb=" O MET 4 717 " (cutoff:3.500A) Processing helix chain '4' and resid 731 through 747 removed outlier: 3.511A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) Processing helix chain '4' and resid 755 through 772 Processing helix chain '4' and resid 783 through 786 No H-bonds generated for 'chain '4' and resid 783 through 786' Processing helix chain '4' and resid 791 through 796 Processing helix chain '5' and resid 22 through 41 Processing helix chain '5' and resid 54 through 65 Processing helix chain '5' and resid 74 through 80 Processing helix chain '5' and resid 82 through 90 Processing helix chain '5' and resid 92 through 111 removed outlier: 3.968A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU 5 98 " --> pdb=" O GLU 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 142 through 144 No H-bonds generated for 'chain '5' and resid 142 through 144' Processing helix chain '5' and resid 251 through 253 No H-bonds generated for 'chain '5' and resid 251 through 253' Processing helix chain '5' and resid 316 through 327 Processing helix chain '5' and resid 331 through 338 Processing helix chain '5' and resid 347 through 358 Processing helix chain '5' and resid 387 through 397 removed outlier: 3.709A pdb=" N LYS 5 396 " --> pdb=" O LYS 5 392 " (cutoff:3.500A) Processing helix chain '5' and resid 411 through 414 No H-bonds generated for 'chain '5' and resid 411 through 414' Processing helix chain '5' and resid 433 through 436 No H-bonds generated for 'chain '5' and resid 433 through 436' Processing helix chain '5' and resid 447 through 449 No H-bonds generated for 'chain '5' and resid 447 through 449' Processing helix chain '5' and resid 452 through 463 removed outlier: 4.149A pdb=" N ALA 5 457 " --> pdb=" O ASP 5 453 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE 5 458 " --> pdb=" O ASP 5 454 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS 5 459 " --> pdb=" O ARG 5 455 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLU 5 460 " --> pdb=" O VAL 5 456 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA 5 461 " --> pdb=" O ALA 5 457 " (cutoff:3.500A) Processing helix chain '5' and resid 500 through 503 Processing helix chain '5' and resid 508 through 513 removed outlier: 3.627A pdb=" N ARG 5 513 " --> pdb=" O THR 5 509 " (cutoff:3.500A) Processing helix chain '5' and resid 526 through 544 removed outlier: 4.057A pdb=" N ALA 5 543 " --> pdb=" O LEU 5 539 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU 5 544 " --> pdb=" O HIS 5 540 " (cutoff:3.500A) Processing helix chain '5' and resid 556 through 569 removed outlier: 3.610A pdb=" N LYS 5 561 " --> pdb=" O ALA 5 557 " (cutoff:3.500A) Processing helix chain '5' and resid 576 through 600 Processing helix chain '5' and resid 610 through 627 removed outlier: 3.767A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 634 through 646 Processing helix chain '6' and resid 21 through 36 Processing helix chain '6' and resid 49 through 54 removed outlier: 3.603A pdb=" N GLU 6 52 " --> pdb=" O LEU 6 49 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 6 54 " --> pdb=" O GLU 6 51 " (cutoff:3.500A) Processing helix chain '6' and resid 65 through 71 Processing helix chain '6' and resid 73 through 81 Processing helix chain '6' and resid 83 through 101 Proline residue: 6 88 - end of helix removed outlier: 4.457A pdb=" N ASP 6 100 " --> pdb=" O THR 6 96 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG 6 101 " --> pdb=" O PHE 6 97 " (cutoff:3.500A) Processing helix chain '6' and resid 123 through 125 No H-bonds generated for 'chain '6' and resid 123 through 125' Processing helix chain '6' and resid 128 through 130 No H-bonds generated for 'chain '6' and resid 128 through 130' Processing helix chain '6' and resid 322 through 328 removed outlier: 3.757A pdb=" N LYS 6 326 " --> pdb=" O ALA 6 322 " (cutoff:3.500A) Processing helix chain '6' and resid 331 through 342 Processing helix chain '6' and resid 346 through 354 Processing helix chain '6' and resid 362 through 373 removed outlier: 3.605A pdb=" N ARG 6 366 " --> pdb=" O ASP 6 362 " (cutoff:3.500A) Processing helix chain '6' and resid 402 through 412 removed outlier: 3.733A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) Processing helix chain '6' and resid 448 through 451 No H-bonds generated for 'chain '6' and resid 448 through 451' Processing helix chain '6' and resid 462 through 464 No H-bonds generated for 'chain '6' and resid 462 through 464' Processing helix chain '6' and resid 467 through 478 removed outlier: 4.509A pdb=" N HIS 6 474 " --> pdb=" O GLN 6 470 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU 6 475 " --> pdb=" O VAL 6 471 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU 6 478 " --> pdb=" O HIS 6 474 " (cutoff:3.500A) Processing helix chain '6' and resid 506 through 508 No H-bonds generated for 'chain '6' and resid 506 through 508' Processing helix chain '6' and resid 516 through 519 No H-bonds generated for 'chain '6' and resid 516 through 519' Processing helix chain '6' and resid 524 through 529 removed outlier: 3.619A pdb=" N ARG 6 529 " --> pdb=" O PRO 6 525 " (cutoff:3.500A) Processing helix chain '6' and resid 542 through 557 Processing helix chain '6' and resid 569 through 581 removed outlier: 4.122A pdb=" N GLN 6 581 " --> pdb=" O LEU 6 577 " (cutoff:3.500A) Processing helix chain '6' and resid 588 through 607 removed outlier: 4.069A pdb=" N SER 6 607 " --> pdb=" O GLN 6 603 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 634 Processing helix chain '6' and resid 642 through 660 Processing helix chain '7' and resid 6 through 19 removed outlier: 3.587A pdb=" N GLU 7 11 " --> pdb=" O ALA 7 7 " (cutoff:3.500A) Processing helix chain '7' and resid 34 through 41 removed outlier: 3.813A pdb=" N ARG 7 39 " --> pdb=" O ASN 7 35 " (cutoff:3.500A) Processing helix chain '7' and resid 52 through 57 removed outlier: 3.720A pdb=" N GLU 7 57 " --> pdb=" O ASP 7 53 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 68 Processing helix chain '7' and resid 70 through 88 Proline residue: 7 86 - end of helix Processing helix chain '7' and resid 101 through 113 Processing helix chain '7' and resid 128 through 131 No H-bonds generated for 'chain '7' and resid 128 through 131' Processing helix chain '7' and resid 149 through 151 No H-bonds generated for 'chain '7' and resid 149 through 151' Processing helix chain '7' and resid 154 through 156 No H-bonds generated for 'chain '7' and resid 154 through 156' Processing helix chain '7' and resid 209 through 214 removed outlier: 3.588A pdb=" N ASN 7 214 " --> pdb=" O GLU 7 210 " (cutoff:3.500A) Processing helix chain '7' and resid 241 through 243 No H-bonds generated for 'chain '7' and resid 241 through 243' Processing helix chain '7' and resid 259 through 261 No H-bonds generated for 'chain '7' and resid 259 through 261' Processing helix chain '7' and resid 286 through 290 Processing helix chain '7' and resid 334 through 336 No H-bonds generated for 'chain '7' and resid 334 through 336' Processing helix chain '7' and resid 343 through 350 removed outlier: 3.766A pdb=" N VAL 7 350 " --> pdb=" O GLY 7 346 " (cutoff:3.500A) Processing helix chain '7' and resid 356 through 365 removed outlier: 4.229A pdb=" N GLY 7 361 " --> pdb=" O LEU 7 357 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 Processing helix chain '7' and resid 433 through 436 No H-bonds generated for 'chain '7' and resid 433 through 436' Processing helix chain '7' and resid 447 through 449 No H-bonds generated for 'chain '7' and resid 447 through 449' Processing helix chain '7' and resid 452 through 464 removed outlier: 3.950A pdb=" N ALA 7 457 " --> pdb=" O ALA 7 453 " (cutoff:3.500A) Processing helix chain '7' and resid 501 through 505 Processing helix chain '7' and resid 509 through 514 removed outlier: 4.343A pdb=" N ARG 7 514 " --> pdb=" O ALA 7 510 " (cutoff:3.500A) Processing helix chain '7' and resid 527 through 543 Processing helix chain '7' and resid 556 through 567 Processing helix chain '7' and resid 575 through 595 removed outlier: 4.164A pdb=" N ASP 7 579 " --> pdb=" O SER 7 576 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER 7 595 " --> pdb=" O ALA 7 592 " (cutoff:3.500A) Processing helix chain '7' and resid 603 through 620 Processing helix chain '7' and resid 627 through 644 Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.525A pdb=" N GLU A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.506A pdb=" N LYS A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 123 through 143 removed outlier: 3.699A pdb=" N ALA A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 273 through 280 removed outlier: 4.491A pdb=" N GLU A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 332 through 351 removed outlier: 4.126A pdb=" N GLN A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.866A pdb=" N ARG A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.938A pdb=" N ASN A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.553A pdb=" N ASP A 466 " --> pdb=" O TRP A 463 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'B' and resid 1392 through 1394 No H-bonds generated for 'chain 'B' and resid 1392 through 1394' Processing helix chain 'B' and resid 1454 through 1462 Processing helix chain 'B' and resid 1486 through 1490 Processing helix chain 'B' and resid 1515 through 1517 No H-bonds generated for 'chain 'B' and resid 1515 through 1517' Processing helix chain 'B' and resid 1574 through 1588 Proline residue: B1582 - end of helix Processing helix chain 'B' and resid 1592 through 1594 No H-bonds generated for 'chain 'B' and resid 1592 through 1594' Processing helix chain 'B' and resid 1619 through 1626 Processing helix chain 'B' and resid 1628 through 1631 No H-bonds generated for 'chain 'B' and resid 1628 through 1631' Processing helix chain 'B' and resid 1650 through 1654 Processing helix chain 'B' and resid 1683 through 1686 No H-bonds generated for 'chain 'B' and resid 1683 through 1686' Processing helix chain 'B' and resid 1691 through 1694 Processing helix chain 'B' and resid 1697 through 1699 No H-bonds generated for 'chain 'B' and resid 1697 through 1699' Processing helix chain 'B' and resid 1702 through 1705 No H-bonds generated for 'chain 'B' and resid 1702 through 1705' Processing helix chain 'B' and resid 1718 through 1732 removed outlier: 3.562A pdb=" N VAL B1725 " --> pdb=" O CYS B1721 " (cutoff:3.500A) Processing helix chain 'B' and resid 1757 through 1763 removed outlier: 4.891A pdb=" N GLN B1762 " --> pdb=" O PHE B1758 " (cutoff:3.500A) Processing helix chain 'B' and resid 1789 through 1792 No H-bonds generated for 'chain 'B' and resid 1789 through 1792' Processing helix chain 'B' and resid 1836 through 1853 removed outlier: 4.323A pdb=" N LEU B1841 " --> pdb=" O LEU B1837 " (cutoff:3.500A) Processing helix chain 'B' and resid 1857 through 1859 No H-bonds generated for 'chain 'B' and resid 1857 through 1859' Processing helix chain 'B' and resid 1862 through 1870 Processing helix chain 'B' and resid 1881 through 1903 removed outlier: 4.066A pdb=" N HIS B1895 " --> pdb=" O THR B1891 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER B1896 " --> pdb=" O SER B1892 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B1897 " --> pdb=" O SER B1893 " (cutoff:3.500A) Processing helix chain 'B' and resid 1925 through 1928 Processing helix chain 'B' and resid 1931 through 1934 No H-bonds generated for 'chain 'B' and resid 1931 through 1934' Processing helix chain 'B' and resid 1990 through 1993 No H-bonds generated for 'chain 'B' and resid 1990 through 1993' Processing helix chain 'B' and resid 1997 through 2018 removed outlier: 3.611A pdb=" N CYS B2010 " --> pdb=" O ALA B2006 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP B2013 " --> pdb=" O HIS B2009 " (cutoff:3.500A) Processing helix chain 'B' and resid 2050 through 2077 removed outlier: 4.824A pdb=" N SER B2077 " --> pdb=" O LYS B2073 " (cutoff:3.500A) Processing helix chain 'B' and resid 2101 through 2113 Processing helix chain 'B' and resid 2120 through 2133 removed outlier: 4.047A pdb=" N ARG B2127 " --> pdb=" O ASN B2123 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B2128 " --> pdb=" O LYS B2124 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2140 through 2142 No H-bonds generated for 'chain 'B' and resid 2140 through 2142' Processing helix chain 'B' and resid 2197 through 2215 removed outlier: 3.696A pdb=" N MET B2201 " --> pdb=" O SER B2197 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B2209 " --> pdb=" O GLU B2205 " (cutoff:3.500A) Processing helix chain 'B' and resid 2248 through 2265 removed outlier: 3.551A pdb=" N GLN B2254 " --> pdb=" O VAL B2250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2268 through 2279 Processing helix chain 'C' and resid 6 through 9 No H-bonds generated for 'chain 'C' and resid 6 through 9' Processing helix chain 'C' and resid 11 through 16 removed outlier: 4.630A pdb=" N SER C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 43 Processing helix chain 'C' and resid 55 through 65 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 106 through 110 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 169 through 189 Processing helix chain 'C' and resid 198 through 209 Processing helix chain 'C' and resid 214 through 229 Processing helix chain 'C' and resid 235 through 254 removed outlier: 3.874A pdb=" N ARG C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 292 Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 305 through 318 removed outlier: 3.865A pdb=" N GLN C 308 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.624A pdb=" N LYS C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.584A pdb=" N LEU C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 436 removed outlier: 3.834A pdb=" N LEU C 409 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS C 435 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C 436 " --> pdb=" O CYS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 463 through 480 Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 522 through 533 removed outlier: 3.815A pdb=" N GLU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 565 Processing helix chain 'D' and resid 4 through 14 removed outlier: 3.812A pdb=" N GLU D 8 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 10 " --> pdb=" O ALA D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 52 Processing helix chain 'D' and resid 59 through 93 removed outlier: 3.766A pdb=" N ARG D 91 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRP D 92 " --> pdb=" O ARG D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 removed outlier: 4.242A pdb=" N HIS D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'D' and resid 179 through 188 removed outlier: 5.264A pdb=" N GLN D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.878A pdb=" N LYS E 12 " --> pdb=" O PHE E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 92 through 103 Processing helix chain 'E' and resid 110 through 138 Processing helix chain 'E' and resid 150 through 172 removed outlier: 3.957A pdb=" N SER E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR E 158 " --> pdb=" O ASN E 154 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 28 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 70 through 76 Processing helix chain 'F' and resid 90 through 92 No H-bonds generated for 'chain 'F' and resid 90 through 92' Processing helix chain 'F' and resid 94 through 102 removed outlier: 3.512A pdb=" N VAL F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 109 through 112 No H-bonds generated for 'chain 'F' and resid 109 through 112' Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.748A pdb=" N LEU F 124 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 155 removed outlier: 4.682A pdb=" N ARG F 147 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 165 No H-bonds generated for 'chain 'F' and resid 162 through 165' Processing helix chain 'F' and resid 170 through 190 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 201 through 204 removed outlier: 4.001A pdb=" N GLN F 204 " --> pdb=" O ASN F 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 204' Processing helix chain 'G' and resid 23 through 39 Processing helix chain 'G' and resid 48 through 67 removed outlier: 3.886A pdb=" N ARG G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 102 Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 124 through 144 Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 158 through 161 No H-bonds generated for 'chain 'G' and resid 158 through 161' Processing helix chain 'G' and resid 190 through 192 No H-bonds generated for 'chain 'G' and resid 190 through 192' Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 212 through 217 Processing helix chain 'H' and resid 668 through 670 No H-bonds generated for 'chain 'H' and resid 668 through 670' Processing helix chain 'H' and resid 722 through 744 removed outlier: 4.068A pdb=" N GLU H 726 " --> pdb=" O LYS H 722 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU H 727 " --> pdb=" O GLY H 723 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER H 732 " --> pdb=" O GLN H 728 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL H 733 " --> pdb=" O PHE H 729 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N HIS H 738 " --> pdb=" O ILE H 734 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU H 739 " --> pdb=" O PHE H 735 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP H 740 " --> pdb=" O HIS H 736 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR H 741 " --> pdb=" O ASN H 737 " (cutoff:3.500A) Processing helix chain 'H' and resid 751 through 774 removed outlier: 3.592A pdb=" N LYS H 759 " --> pdb=" O ASN H 755 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN H 762 " --> pdb=" O THR H 758 " (cutoff:3.500A) Processing helix chain 'H' and resid 778 through 785 Processing helix chain 'H' and resid 790 through 802 Processing helix chain 'H' and resid 806 through 822 removed outlier: 4.302A pdb=" N LYS H 811 " --> pdb=" O ILE H 807 " (cutoff:3.500A) Processing helix chain 'I' and resid 721 through 745 removed outlier: 3.859A pdb=" N GLU I 726 " --> pdb=" O LYS I 722 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N HIS I 738 " --> pdb=" O ILE I 734 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU I 739 " --> pdb=" O PHE I 735 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP I 740 " --> pdb=" O HIS I 736 " (cutoff:3.500A) Processing helix chain 'I' and resid 751 through 774 Processing helix chain 'I' and resid 779 through 787 removed outlier: 4.392A pdb=" N LEU I 787 " --> pdb=" O GLU I 783 " (cutoff:3.500A) Processing helix chain 'I' and resid 790 through 801 removed outlier: 4.719A pdb=" N LYS I 798 " --> pdb=" O ASN I 794 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR I 799 " --> pdb=" O LEU I 795 " (cutoff:3.500A) Processing helix chain 'I' and resid 806 through 822 Processing helix chain 'I' and resid 1021 through 1036 removed outlier: 5.350A pdb=" N SER I1031 " --> pdb=" O GLU I1027 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASN I1032 " --> pdb=" O GLU I1028 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP I1036 " --> pdb=" O ASN I1032 " (cutoff:3.500A) Processing helix chain 'I' and resid 1043 through 1055 removed outlier: 3.804A pdb=" N ILE I1052 " --> pdb=" O LYS I1048 " (cutoff:3.500A) Processing helix chain 'I' and resid 1059 through 1068 removed outlier: 3.634A pdb=" N LYS I1063 " --> pdb=" O THR I1059 " (cutoff:3.500A) Processing helix chain 'J' and resid 652 through 654 No H-bonds generated for 'chain 'J' and resid 652 through 654' Processing helix chain 'J' and resid 664 through 667 No H-bonds generated for 'chain 'J' and resid 664 through 667' Processing helix chain 'J' and resid 721 through 745 removed outlier: 4.085A pdb=" N ILE J 734 " --> pdb=" O TRP J 730 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS J 736 " --> pdb=" O SER J 732 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS J 738 " --> pdb=" O ILE J 734 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU J 739 " --> pdb=" O PHE J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 751 through 774 removed outlier: 3.501A pdb=" N ALA J 757 " --> pdb=" O THR J 753 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN J 762 " --> pdb=" O THR J 758 " (cutoff:3.500A) Processing helix chain 'J' and resid 778 through 787 removed outlier: 4.600A pdb=" N LEU J 787 " --> pdb=" O GLU J 783 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 801 Processing helix chain 'J' and resid 806 through 820 Processing helix chain 'K' and resid 8 through 17 Processing helix chain 'K' and resid 29 through 43 removed outlier: 4.566A pdb=" N LEU K 32 " --> pdb=" O PRO K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 58 Processing helix chain 'K' and resid 60 through 63 No H-bonds generated for 'chain 'K' and resid 60 through 63' Processing helix chain 'K' and resid 65 through 71 Processing helix chain 'K' and resid 76 through 90 Processing helix chain 'K' and resid 93 through 97 Processing helix chain 'K' and resid 104 through 125 removed outlier: 3.859A pdb=" N ALA K 125 " --> pdb=" O LYS K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 141 Processing helix chain 'K' and resid 145 through 147 No H-bonds generated for 'chain 'K' and resid 145 through 147' Processing helix chain 'K' and resid 151 through 168 Processing helix chain 'K' and resid 173 through 179 removed outlier: 4.389A pdb=" N LYS K 178 " --> pdb=" O ASP K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 196 Processing helix chain 'K' and resid 198 through 207 Processing helix chain 'K' and resid 212 through 225 removed outlier: 4.980A pdb=" N LEU K 216 " --> pdb=" O GLN K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 235 Processing helix chain 'K' and resid 239 through 270 removed outlier: 4.637A pdb=" N LEU K 242 " --> pdb=" O GLN K 239 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA K 243 " --> pdb=" O GLY K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 305 removed outlier: 3.669A pdb=" N ARG K 305 " --> pdb=" O HIS K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 320 through 322 No H-bonds generated for 'chain 'K' and resid 320 through 322' Processing helix chain 'K' and resid 336 through 352 Processing helix chain 'K' and resid 354 through 367 Processing helix chain 'K' and resid 374 through 391 removed outlier: 3.648A pdb=" N MET K 386 " --> pdb=" O LEU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 399 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 426 through 455 removed outlier: 6.264A pdb=" N ALA K 430 " --> pdb=" O LYS K 427 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL K 450 " --> pdb=" O LEU K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 474 Processing helix chain 'K' and resid 476 through 488 removed outlier: 4.800A pdb=" N PHE K 482 " --> pdb=" O TYR K 478 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU K 483 " --> pdb=" O ARG K 479 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS K 488 " --> pdb=" O ALA K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 519 Processing helix chain 'K' and resid 691 through 699 removed outlier: 3.953A pdb=" N ARG K 697 " --> pdb=" O ASP K 693 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE K 698 " --> pdb=" O TYR K 694 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA K 699 " --> pdb=" O LEU K 695 " (cutoff:3.500A) Processing helix chain 'K' and resid 701 through 713 removed outlier: 4.459A pdb=" N SER K 713 " --> pdb=" O LEU K 709 " (cutoff:3.500A) Processing helix chain 'K' and resid 719 through 734 Processing helix chain 'K' and resid 739 through 742 No H-bonds generated for 'chain 'K' and resid 739 through 742' Processing helix chain 'K' and resid 745 through 756 Processing helix chain 'K' and resid 760 through 783 removed outlier: 3.834A pdb=" N LYS K 764 " --> pdb=" O GLY K 761 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU K 765 " --> pdb=" O ALA K 762 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL K 767 " --> pdb=" O LYS K 764 " (cutoff:3.500A) Processing helix chain 'K' and resid 785 through 792 removed outlier: 3.510A pdb=" N LEU K 791 " --> pdb=" O PHE K 788 " (cutoff:3.500A) Processing helix chain 'K' and resid 797 through 802 Processing helix chain 'L' and resid 78 through 84 removed outlier: 3.918A pdb=" N HIS L 83 " --> pdb=" O PRO L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 114 Processing helix chain 'L' and resid 120 through 132 removed outlier: 3.876A pdb=" N TYR L 129 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 145 Processing helix chain 'O' and resid 13 through 16 No H-bonds generated for 'chain 'O' and resid 13 through 16' Processing helix chain 'O' and resid 97 through 112 Processing helix chain 'O' and resid 171 through 174 No H-bonds generated for 'chain 'O' and resid 171 through 174' Processing helix chain 'O' and resid 195 through 198 Processing helix chain 'O' and resid 218 through 221 Processing helix chain 'O' and resid 223 through 227 Processing helix chain 'O' and resid 243 through 247 removed outlier: 3.576A pdb=" N CYS O 246 " --> pdb=" O VAL O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 268 through 270 No H-bonds generated for 'chain 'O' and resid 268 through 270' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.676A pdb=" N ARG O 292 " --> pdb=" O SER O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 321 through 331 removed outlier: 3.760A pdb=" N THR O 330 " --> pdb=" O SER O 326 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE O 331 " --> pdb=" O SER O 327 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 352 Processing helix chain 'O' and resid 355 through 358 No H-bonds generated for 'chain 'O' and resid 355 through 358' Processing helix chain 'O' and resid 376 through 378 No H-bonds generated for 'chain 'O' and resid 376 through 378' Processing helix chain 'O' and resid 403 through 411 Processing helix chain 'P' and resid 24 through 35 removed outlier: 3.768A pdb=" N ILE P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 41 No H-bonds generated for 'chain 'P' and resid 39 through 41' Processing helix chain 'P' and resid 57 through 59 No H-bonds generated for 'chain 'P' and resid 57 through 59' Processing helix chain 'P' and resid 69 through 71 No H-bonds generated for 'chain 'P' and resid 69 through 71' Processing helix chain 'R' and resid 33 through 38 Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 67 through 80 removed outlier: 3.581A pdb=" N TYR R 79 " --> pdb=" O MET R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 110 removed outlier: 3.869A pdb=" N LEU R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 24 removed outlier: 3.858A pdb=" N ALA S 23 " --> pdb=" O THR S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 46 removed outlier: 3.559A pdb=" N PHE S 39 " --> pdb=" O TRP S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 78 Processing helix chain 'S' and resid 83 through 104 removed outlier: 3.919A pdb=" N ARG S 89 " --> pdb=" O VAL S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 112 Processing helix chain 'S' and resid 139 through 150 removed outlier: 3.927A pdb=" N LYS S 149 " --> pdb=" O ASP S 145 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU S 150 " --> pdb=" O MET S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 154 through 168 removed outlier: 3.507A pdb=" N ILE S 158 " --> pdb=" O LEU S 155 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG S 161 " --> pdb=" O ILE S 158 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU S 164 " --> pdb=" O ARG S 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 188 Processing helix chain 'S' and resid 199 through 206 Processing helix chain 'S' and resid 208 through 229 Processing helix chain 'S' and resid 232 through 253 Processing helix chain 'S' and resid 259 through 270 removed outlier: 3.652A pdb=" N ARG S 269 " --> pdb=" O GLU S 265 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 286 removed outlier: 4.295A pdb=" N HIS S 283 " --> pdb=" O HIS S 279 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN S 284 " --> pdb=" O ALA S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 303 removed outlier: 4.636A pdb=" N ALA S 303 " --> pdb=" O VAL S 299 " (cutoff:3.500A) Processing helix chain 'S' and resid 305 through 330 Proline residue: S 309 - end of helix removed outlier: 4.584A pdb=" N LEU S 330 " --> pdb=" O ALA S 326 " (cutoff:3.500A) Processing helix chain 'S' and resid 336 through 357 Processing helix chain 'S' and resid 362 through 376 Processing helix chain 'S' and resid 387 through 399 Processing helix chain 'S' and resid 411 through 424 removed outlier: 3.792A pdb=" N ILE S 419 " --> pdb=" O LEU S 415 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR S 420 " --> pdb=" O THR S 416 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL S 421 " --> pdb=" O SER S 417 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR S 424 " --> pdb=" O THR S 420 " (cutoff:3.500A) Processing helix chain 'S' and resid 428 through 444 removed outlier: 3.625A pdb=" N MET S 438 " --> pdb=" O PHE S 434 " (cutoff:3.500A) Processing helix chain 'S' and resid 451 through 465 Processing helix chain 'S' and resid 471 through 496 removed outlier: 4.080A pdb=" N MET S 480 " --> pdb=" O MET S 476 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER S 481 " --> pdb=" O TYR S 477 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN S 488 " --> pdb=" O ALA S 484 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS S 489 " --> pdb=" O ASP S 485 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN S 492 " --> pdb=" O ASN S 488 " (cutoff:3.500A) Processing helix chain 'S' and resid 537 through 547 Processing helix chain 'S' and resid 557 through 559 No H-bonds generated for 'chain 'S' and resid 557 through 559' Processing helix chain 'S' and resid 596 through 600 Processing helix chain 'S' and resid 607 through 618 removed outlier: 4.504A pdb=" N LYS S 612 " --> pdb=" O LYS S 608 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR S 613 " --> pdb=" O GLU S 609 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE S 614 " --> pdb=" O LEU S 610 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N SER S 616 " --> pdb=" O THR S 611 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU S 617 " --> pdb=" O LYS S 612 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU S 618 " --> pdb=" O THR S 613 " (cutoff:3.500A) Processing helix chain 'S' and resid 662 through 690 removed outlier: 4.382A pdb=" N SER S 670 " --> pdb=" O GLU S 666 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA S 671 " --> pdb=" O GLN S 667 " (cutoff:3.500A) Processing helix chain 'S' and resid 696 through 699 No H-bonds generated for 'chain 'S' and resid 696 through 699' Processing helix chain 'S' and resid 702 through 707 Processing helix chain 'S' and resid 715 through 728 removed outlier: 3.993A pdb=" N VAL S 724 " --> pdb=" O LYS S 720 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP S 727 " --> pdb=" O GLU S 723 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 59 Processing helix chain 'T' and resid 81 through 88 Processing sheet with id= A, first strand: chain '2' and resid 229 through 233 removed outlier: 6.286A pdb=" N HIS 2 282 " --> pdb=" O LEU 2 230 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL 2 232 " --> pdb=" O HIS 2 282 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG 2 284 " --> pdb=" O VAL 2 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 393 through 399 removed outlier: 6.559A pdb=" N GLN 2 379 " --> pdb=" O VAL 2 312 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL 2 312 " --> pdb=" O GLN 2 379 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE 2 417 " --> pdb=" O ALA 2 441 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA 2 441 " --> pdb=" O ILE 2 417 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS 2 419 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE 2 439 " --> pdb=" O HIS 2 419 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASN 2 421 " --> pdb=" O THR 2 437 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR 2 437 " --> pdb=" O ASN 2 421 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 659 through 663 Processing sheet with id= D, first strand: chain '2' and resid 558 through 562 Processing sheet with id= E, first strand: chain '2' and resid 608 through 613 Processing sheet with id= F, first strand: chain '2' and resid 319 through 324 removed outlier: 6.957A pdb=" N ILE 2 369 " --> pdb=" O SER 2 323 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 46 through 50 removed outlier: 6.572A pdb=" N TYR 3 99 " --> pdb=" O LEU 3 47 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL 3 49 " --> pdb=" O TYR 3 99 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY 3 101 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain '3' and resid 234 through 240 removed outlier: 6.459A pdb=" N THR 3 200 " --> pdb=" O THR 3 132 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS 3 134 " --> pdb=" O THR 3 198 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR 3 198 " --> pdb=" O CYS 3 134 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR 3 258 " --> pdb=" O SER 3 216 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP 3 218 " --> pdb=" O THR 3 258 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP 3 222 " --> pdb=" O ALA 3 262 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ASN 3 264 " --> pdb=" O ASP 3 222 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG 3 257 " --> pdb=" O LEU 3 244 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL 3 238 " --> pdb=" O CYS 3 263 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL 3 265 " --> pdb=" O GLN 3 236 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN 3 236 " --> pdb=" O VAL 3 265 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 153 through 158 removed outlier: 3.690A pdb=" N LYS 3 153 " --> pdb=" O CYS 3 148 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL 3 145 " --> pdb=" O GLU 3 187 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 481 through 485 Processing sheet with id= K, first strand: chain '3' and resid 380 through 384 Processing sheet with id= L, first strand: chain '3' and resid 430 through 434 Processing sheet with id= M, first strand: chain '3' and resid 138 through 143 removed outlier: 6.791A pdb=" N VAL 3 192 " --> pdb=" O VAL 3 142 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 207 through 211 removed outlier: 6.488A pdb=" N GLN 4 259 " --> pdb=" O LEU 4 208 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL 4 210 " --> pdb=" O GLN 4 259 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ARG 4 261 " --> pdb=" O VAL 4 210 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain '4' and resid 369 through 375 removed outlier: 5.996A pdb=" N GLN 4 355 " --> pdb=" O VAL 4 289 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL 4 289 " --> pdb=" O GLN 4 355 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN 4 281 " --> pdb=" O TYR 4 394 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE 4 393 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 393 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG 4 395 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE 4 416 " --> pdb=" O ARG 4 395 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL 4 397 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N THR 4 414 " --> pdb=" O VAL 4 397 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '4' and resid 312 through 316 Processing sheet with id= Q, first strand: chain '4' and resid 646 through 649 removed outlier: 6.259A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 546 through 549 Processing sheet with id= S, first strand: chain '4' and resid 595 through 599 Processing sheet with id= T, first strand: chain '4' and resid 296 through 301 removed outlier: 6.633A pdb=" N LEU 4 345 " --> pdb=" O GLN 4 300 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '5' and resid 44 through 46 Processing sheet with id= V, first strand: chain '5' and resid 69 through 73 removed outlier: 6.133A pdb=" N GLN 5 125 " --> pdb=" O ILE 5 70 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL 5 72 " --> pdb=" O GLN 5 125 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET 5 127 " --> pdb=" O VAL 5 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain '5' and resid 244 through 250 removed outlier: 3.724A pdb=" N ALA 5 157 " --> pdb=" O LYS 5 228 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN 5 230 " --> pdb=" O ILE 5 155 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE 5 155 " --> pdb=" O GLN 5 230 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE 5 268 " --> pdb=" O VAL 5 296 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL 5 296 " --> pdb=" O ILE 5 268 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER 5 270 " --> pdb=" O ILE 5 294 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE 5 294 " --> pdb=" O SER 5 270 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 170 through 172 Processing sheet with id= Y, first strand: chain '5' and resid 516 through 520 Processing sheet with id= Z, first strand: chain '5' and resid 416 through 420 Processing sheet with id= AA, first strand: chain '5' and resid 466 through 471 Processing sheet with id= AB, first strand: chain '5' and resid 162 through 167 removed outlier: 6.811A pdb=" N LYS 5 220 " --> pdb=" O THR 5 166 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '6' and resid 60 through 64 removed outlier: 6.583A pdb=" N TYR 6 111 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL 6 63 " --> pdb=" O TYR 6 111 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA 6 113 " --> pdb=" O VAL 6 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain '6' and resid 241 through 247 removed outlier: 6.607A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR 6 144 " --> pdb=" O LYS 6 205 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS 6 205 " --> pdb=" O THR 6 144 " (cutoff:3.500A) removed outlier: 14.766A pdb=" N TYR 6 294 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N GLU 6 225 " --> pdb=" O TYR 6 294 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU 6 296 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ILE 6 227 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE 6 298 " --> pdb=" O ILE 6 227 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ARG 6 229 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA 6 300 " --> pdb=" O ARG 6 229 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR 6 245 " --> pdb=" O CYS 6 301 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL 6 303 " --> pdb=" O ASP 6 243 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP 6 243 " --> pdb=" O VAL 6 303 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '6' and resid 156 through 158 Processing sheet with id= AF, first strand: chain '6' and resid 532 through 536 removed outlier: 6.531A pdb=" N VAL 6 417 " --> pdb=" O CYS 6 458 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASP 6 460 " --> pdb=" O VAL 6 417 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR 6 419 " --> pdb=" O ASP 6 460 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 431 through 435 Processing sheet with id= AH, first strand: chain '6' and resid 481 through 486 Processing sheet with id= AI, first strand: chain '6' and resid 148 through 153 removed outlier: 7.145A pdb=" N ARG 6 199 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '7' and resid 47 through 51 removed outlier: 6.548A pdb=" N GLU 7 135 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL 7 50 " --> pdb=" O GLU 7 135 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR 7 137 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain '7' and resid 270 through 276 removed outlier: 6.379A pdb=" N LYS 7 236 " --> pdb=" O THR 7 168 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL 7 170 " --> pdb=" O GLU 7 234 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLU 7 234 " --> pdb=" O VAL 7 170 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N THR 7 296 " --> pdb=" O SER 7 252 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR 7 254 " --> pdb=" O THR 7 296 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU 7 258 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ARG 7 302 " --> pdb=" O GLU 7 258 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR 7 274 " --> pdb=" O HIS 7 301 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE 7 303 " --> pdb=" O SER 7 272 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER 7 272 " --> pdb=" O ILE 7 303 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 190 through 194 Processing sheet with id= AM, first strand: chain '7' and resid 517 through 520 Processing sheet with id= AN, first strand: chain '7' and resid 417 through 419 Processing sheet with id= AO, first strand: chain '7' and resid 466 through 470 Processing sheet with id= AP, first strand: chain '7' and resid 174 through 179 removed outlier: 6.580A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'A' and resid 86 through 90 removed outlier: 6.681A pdb=" N LEU A 477 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N PHE A 415 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 479 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 495 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 480 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'A' and resid 97 through 100 Processing sheet with id= AS, first strand: chain 'A' and resid 202 through 205 removed outlier: 4.022A pdb=" N LYS A 191 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 196 " --> pdb=" O GLN A 189 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLN A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU A 198 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE A 187 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 241 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP A 229 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 237 " --> pdb=" O TRP A 229 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 231 " --> pdb=" O PHE A 235 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'A' and resid 518 through 520 removed outlier: 4.011A pdb=" N VAL A 511 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS A 318 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LEU A 290 " --> pdb=" O CYS A 318 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 320 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG A 360 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU A 321 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 362 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 1426 through 1428 removed outlier: 5.321A pdb=" N HIS B1410 " --> pdb=" O PHE B1476 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N PHE B1476 " --> pdb=" O HIS B1410 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'B' and resid 1535 through 1539 Processing sheet with id= AW, first strand: chain 'B' and resid 1785 through 1787 removed outlier: 3.730A pdb=" N GLU B1949 " --> pdb=" O LEU B1787 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'B' and resid 1968 through 1970 removed outlier: 3.666A pdb=" N GLU B1969 " --> pdb=" O LEU B1986 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'B' and resid 2219 through 2221 Processing sheet with id= AZ, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.359A pdb=" N VAL C 19 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL C 50 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU C 21 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 52 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL C 23 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR C 71 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE C 22 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE C 73 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ALA C 24 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE C 75 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 94 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU C 74 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE C 96 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'C' and resid 269 through 276 Processing sheet with id= BB, first strand: chain 'C' and resid 445 through 449 removed outlier: 8.153A pdb=" N CYS C 448 " --> pdb=" O PRO C 490 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 492 " --> pdb=" O CYS C 448 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR C 503 " --> pdb=" O LEU C 497 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'D' and resid 174 through 178 Processing sheet with id= BD, first strand: chain 'D' and resid 158 through 160 Processing sheet with id= BE, first strand: chain 'E' and resid 41 through 45 Processing sheet with id= BF, first strand: chain 'F' and resid 65 through 69 Processing sheet with id= BG, first strand: chain 'G' and resid 203 through 207 Processing sheet with id= BH, first strand: chain 'G' and resid 182 through 184 Processing sheet with id= BI, first strand: chain 'H' and resid 479 through 481 removed outlier: 5.127A pdb=" N CYS H 457 " --> pdb=" O PHE H 446 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE H 446 " --> pdb=" O CYS H 457 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN H 459 " --> pdb=" O HIS H 444 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N HIS H 444 " --> pdb=" O ASN H 459 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'H' and resid 489 through 492 Processing sheet with id= BK, first strand: chain 'H' and resid 566 through 568 removed outlier: 3.854A pdb=" N LEU H 553 " --> pdb=" O THR H 549 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA H 537 " --> pdb=" O ALA H 548 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'H' and resid 573 through 579 removed outlier: 7.289A pdb=" N VAL H 586 " --> pdb=" O VAL H 574 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N MET H 576 " --> pdb=" O PHE H 584 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE H 584 " --> pdb=" O MET H 576 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY H 578 " --> pdb=" O GLN H 582 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN H 582 " --> pdb=" O GLY H 578 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU H 603 " --> pdb=" O HIS H 615 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS H 615 " --> pdb=" O LEU H 603 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'H' and resid 627 through 632 removed outlier: 6.643A pdb=" N VAL H 641 " --> pdb=" O ALA H 628 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE H 630 " --> pdb=" O CYS H 639 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N CYS H 639 " --> pdb=" O ILE H 630 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE H 646 " --> pdb=" O ASP H 642 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET H 649 " --> pdb=" O PRO H 660 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN H 651 " --> pdb=" O TRP H 658 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TRP H 658 " --> pdb=" O ASN H 651 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'H' and resid 706 through 709 removed outlier: 6.153A pdb=" N ILE H 690 " --> pdb=" O VAL H 677 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL H 677 " --> pdb=" O ILE H 690 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS H 692 " --> pdb=" O TYR H 675 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR H 675 " --> pdb=" O CYS H 692 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'I' and resid 479 through 482 removed outlier: 6.326A pdb=" N CYS I 457 " --> pdb=" O PHE I 446 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE I 446 " --> pdb=" O CYS I 457 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ASN I 459 " --> pdb=" O HIS I 444 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS I 444 " --> pdb=" O ASN I 459 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'I' and resid 489 through 492 Processing sheet with id= BQ, first strand: chain 'I' and resid 566 through 568 removed outlier: 3.763A pdb=" N LEU I 553 " --> pdb=" O THR I 549 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'I' and resid 573 through 579 removed outlier: 6.991A pdb=" N VAL I 586 " --> pdb=" O VAL I 574 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET I 576 " --> pdb=" O PHE I 584 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE I 584 " --> pdb=" O MET I 576 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY I 578 " --> pdb=" O GLN I 582 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN I 582 " --> pdb=" O GLY I 578 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU I 614 " --> pdb=" O LEU I 603 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU I 605 " --> pdb=" O GLN I 612 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN I 612 " --> pdb=" O GLU I 605 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'I' and resid 627 through 632 removed outlier: 6.682A pdb=" N VAL I 641 " --> pdb=" O ALA I 628 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE I 630 " --> pdb=" O CYS I 639 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS I 639 " --> pdb=" O ILE I 630 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS I 662 " --> pdb=" O VAL I 647 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N MET I 649 " --> pdb=" O PRO I 660 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN I 651 " --> pdb=" O TRP I 658 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TRP I 658 " --> pdb=" O ASN I 651 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'I' and resid 707 through 709 removed outlier: 6.309A pdb=" N ILE I 690 " --> pdb=" O VAL I 677 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL I 677 " --> pdb=" O ILE I 690 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS I 692 " --> pdb=" O TYR I 675 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR I 675 " --> pdb=" O CYS I 692 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'J' and resid 464 through 470 removed outlier: 3.625A pdb=" N VAL J 448 " --> pdb=" O ILE J 455 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS J 457 " --> pdb=" O PHE J 446 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N PHE J 446 " --> pdb=" O CYS J 457 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASN J 459 " --> pdb=" O HIS J 444 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N HIS J 444 " --> pdb=" O ASN J 459 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'J' and resid 489 through 492 Processing sheet with id= BW, first strand: chain 'J' and resid 537 through 541 removed outlier: 3.772A pdb=" N ALA J 537 " --> pdb=" O ALA J 548 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP J 544 " --> pdb=" O GLY J 541 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU J 553 " --> pdb=" O THR J 549 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'J' and resid 600 through 605 removed outlier: 5.860A pdb=" N HIS J 588 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL J 573 " --> pdb=" O HIS J 588 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'J' and resid 707 through 709 removed outlier: 6.427A pdb=" N ILE J 690 " --> pdb=" O VAL J 677 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL J 677 " --> pdb=" O ILE J 690 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS J 692 " --> pdb=" O TYR J 675 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TYR J 675 " --> pdb=" O CYS J 692 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'J' and resid 627 through 632 removed outlier: 6.787A pdb=" N VAL J 641 " --> pdb=" O ALA J 628 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE J 630 " --> pdb=" O CYS J 639 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N CYS J 639 " --> pdb=" O ILE J 630 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'J' and resid 646 through 651 removed outlier: 3.579A pdb=" N CYS J 662 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N MET J 649 " --> pdb=" O PRO J 660 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASN J 651 " --> pdb=" O TRP J 658 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP J 658 " --> pdb=" O ASN J 651 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.585A pdb=" N TYR K 19 " --> pdb=" O HIS K 26 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'K' and resid 282 through 288 removed outlier: 3.788A pdb=" N LEU K 295 " --> pdb=" O VAL K 284 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'O' and resid 58 through 61 removed outlier: 4.158A pdb=" N LYS O 94 " --> pdb=" O GLU O 6 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLU O 8 " --> pdb=" O LEU O 92 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU O 92 " --> pdb=" O GLU O 8 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE O 10 " --> pdb=" O ILE O 90 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE O 90 " --> pdb=" O ILE O 10 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'O' and resid 137 through 140 removed outlier: 6.649A pdb=" N HIS O 158 " --> pdb=" O MET O 138 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE O 140 " --> pdb=" O HIS O 158 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN O 160 " --> pdb=" O ILE O 140 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS O 181 " --> pdb=" O LEU O 159 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR O 161 " --> pdb=" O LYS O 181 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP O 183 " --> pdb=" O THR O 161 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU O 204 " --> pdb=" O LEU O 182 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER O 230 " --> pdb=" O LEU O 205 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASN O 253 " --> pdb=" O LEU O 231 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE O 276 " --> pdb=" O LEU O 254 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR O 298 " --> pdb=" O LEU O 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= CE Processing sheet with id= CF, first strand: chain 'O' and resid 369 through 375 Processing sheet with id= CG, first strand: chain 'P' and resid 5 through 7 Processing sheet with id= CH, first strand: chain 'R' and resid 28 through 32 Processing sheet with id= CI, first strand: chain 'T' and resid 70 through 72 3109 hydrogen bonds defined for protein. 8581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 32.18 Time building geometry restraints manager: 27.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 26056 1.35 - 1.48: 19125 1.48 - 1.61: 34517 1.61 - 1.74: 8 1.74 - 1.87: 744 Bond restraints: 80450 Sorted by residual: bond pdb=" O3A ANP 31500 " pdb=" PB ANP 31500 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" O3A ANP 21003 " pdb=" PB ANP 21003 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP 5 801 " pdb=" PB ANP 5 801 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" N3B ANP 31500 " pdb=" PG ANP 31500 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N3B ANP 5 801 " pdb=" PG ANP 5 801 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.75e+01 ... (remaining 80445 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.59: 1904 105.59 - 113.40: 43516 113.40 - 121.21: 41803 121.21 - 129.02: 20933 129.02 - 136.83: 742 Bond angle restraints: 108898 Sorted by residual: angle pdb=" N PRO B2183 " pdb=" CA PRO B2183 " pdb=" CB PRO B2183 " ideal model delta sigma weight residual 102.28 110.05 -7.77 7.50e-01 1.78e+00 1.07e+02 angle pdb=" C GLY O 391 " pdb=" N THR O 392 " pdb=" CA THR O 392 " ideal model delta sigma weight residual 122.60 136.83 -14.23 1.56e+00 4.11e-01 8.32e+01 angle pdb=" CA ILE Q 297 " pdb=" CB ILE Q 297 " pdb=" CG2 ILE Q 297 " ideal model delta sigma weight residual 110.50 120.07 -9.57 1.70e+00 3.46e-01 3.17e+01 angle pdb=" C GLU S 174 " pdb=" N ASP S 175 " pdb=" CA ASP S 175 " ideal model delta sigma weight residual 121.70 131.05 -9.35 1.80e+00 3.09e-01 2.70e+01 angle pdb=" C VAL T 38 " pdb=" N VAL T 39 " pdb=" CA VAL T 39 " ideal model delta sigma weight residual 121.70 130.52 -8.82 1.80e+00 3.09e-01 2.40e+01 ... (remaining 108893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.99: 47602 30.99 - 61.98: 1322 61.98 - 92.97: 173 92.97 - 123.96: 1 123.96 - 154.94: 2 Dihedral angle restraints: 49100 sinusoidal: 20523 harmonic: 28577 Sorted by residual: dihedral pdb=" CB CYS B2161 " pdb=" SG CYS B2161 " pdb=" SG CYS B2190 " pdb=" CB CYS B2190 " ideal model delta sinusoidal sigma weight residual 93.00 8.31 84.69 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS B2158 " pdb=" SG CYS B2158 " pdb=" SG CYS B2190 " pdb=" CB CYS B2190 " ideal model delta sinusoidal sigma weight residual -86.00 -155.76 69.76 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS B2161 " pdb=" SG CYS B2161 " pdb=" SG CYS B2187 " pdb=" CB CYS B2187 " ideal model delta sinusoidal sigma weight residual -86.00 -154.15 68.15 1 1.00e+01 1.00e-02 6.03e+01 ... (remaining 49097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 9413 0.053 - 0.106: 2288 0.106 - 0.159: 451 0.159 - 0.212: 47 0.212 - 0.264: 5 Chirality restraints: 12204 Sorted by residual: chirality pdb=" C3' ANP 5 801 " pdb=" C2' ANP 5 801 " pdb=" C4' ANP 5 801 " pdb=" O3' ANP 5 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C3' ANP 21003 " pdb=" C2' ANP 21003 " pdb=" C4' ANP 21003 " pdb=" O3' ANP 21003 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA PRO B2183 " pdb=" N PRO B2183 " pdb=" C PRO B2183 " pdb=" CB PRO B2183 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 12201 not shown) Planarity restraints: 13869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE S 614 " -0.037 2.00e-02 2.50e+03 7.24e-02 5.25e+01 pdb=" C ILE S 614 " 0.125 2.00e-02 2.50e+03 pdb=" O ILE S 614 " -0.048 2.00e-02 2.50e+03 pdb=" N SER S 616 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER 7 365 " 0.060 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO 7 366 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO 7 366 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO 7 366 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR 6 46 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C TYR 6 46 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR 6 46 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU 6 47 " 0.020 2.00e-02 2.50e+03 ... (remaining 13866 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.87: 9 1.87 - 2.63: 541 2.63 - 3.39: 106338 3.39 - 4.14: 195521 4.14 - 4.90: 351458 Nonbonded interactions: 653867 Sorted by model distance: nonbonded pdb=" CH2 TRP Q 536 " pdb=" OE1 GLU 6 323 " model vdw 1.116 3.340 nonbonded pdb=" CE2 PHE Q 535 " pdb=" NZ LYS 6 326 " model vdw 1.400 3.420 nonbonded pdb=" NE2 GLN Q 294 " pdb=" CG ASN K 522 " model vdw 1.429 3.350 nonbonded pdb=" CZ3 TRP Q 536 " pdb=" CD LYS 6 326 " model vdw 1.443 3.740 nonbonded pdb=" CZ2 TRP Q 536 " pdb=" OE1 GLU 6 323 " model vdw 1.451 3.340 ... (remaining 653862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'H' and (resid 423 through 466 or resid 468 through 809 or resid 811 thro \ ugh 823)) selection = (chain 'I' and (resid 423 through 466 or resid 468 through 809 or resid 811 thro \ ugh 823)) selection = (chain 'J' and (resid 423 through 466 or resid 468 through 809 or resid 811 thro \ ugh 823)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.400 Construct map_model_manager: 0.070 Extract box with map and model: 15.390 Check model and map are aligned: 0.910 Set scattering table: 0.590 Process input model: 184.580 Find NCS groups from input model: 4.000 Set up NCS constraints: 0.310 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:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 218.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.006 0.149 80450 Z= 0.364 Angle : 0.895 14.228 108898 Z= 0.483 Chirality : 0.048 0.264 12204 Planarity : 0.007 0.098 13869 Dihedral : 14.474 154.944 30487 Min Nonbonded Distance : 1.116 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.82 % Favored : 95.08 % Rotamer: Outliers : 1.06 % Allowed : 5.45 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.08), residues: 9604 helix: 0.25 (0.08), residues: 4165 sheet: -0.62 (0.14), residues: 1271 loop : -0.94 (0.09), residues: 4168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 676 HIS 0.015 0.002 HIS O 381 PHE 0.026 0.002 PHE 2 834 TYR 0.027 0.002 TYR 6 546 ARG 0.006 0.001 ARG 3 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1088 time to evaluate : 7.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 315 HIS cc_start: 0.5009 (OUTLIER) cc_final: 0.4795 (m-70) REVERT: 3 268 MET cc_start: 0.7570 (mtm) cc_final: 0.7287 (mtp) REVERT: 4 266 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7837 (pt) REVERT: 5 516 MET cc_start: 0.8423 (mtm) cc_final: 0.8165 (mtp) REVERT: 6 334 TRP cc_start: 0.7689 (OUTLIER) cc_final: 0.7071 (t-100) REVERT: 6 438 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7534 (mt-10) REVERT: 6 465 MET cc_start: 0.7946 (mtm) cc_final: 0.7671 (mtm) REVERT: 7 205 MET cc_start: 0.8973 (mmm) cc_final: 0.8555 (mmm) REVERT: 7 407 ARG cc_start: 0.4345 (pmt-80) cc_final: 0.4101 (pmt170) REVERT: 7 609 ILE cc_start: 0.9385 (mm) cc_final: 0.8920 (pt) REVERT: A 417 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: B 1754 MET cc_start: 0.4065 (mmt) cc_final: 0.3522 (mtt) REVERT: C 174 ARG cc_start: 0.7224 (tpt170) cc_final: 0.6990 (tpt170) REVERT: C 332 MET cc_start: 0.8537 (ttm) cc_final: 0.8280 (ttm) REVERT: D 156 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: E 68 VAL cc_start: 0.8701 (t) cc_final: 0.8464 (m) REVERT: F 30 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7549 (mm-30) REVERT: F 78 ASP cc_start: 0.7189 (p0) cc_final: 0.6820 (p0) REVERT: F 127 ASP cc_start: 0.7677 (t0) cc_final: 0.7454 (t0) REVERT: H 640 TYR cc_start: 0.3806 (p90) cc_final: 0.3516 (p90) REVERT: H 777 ARG cc_start: 0.7457 (mtt-85) cc_final: 0.7094 (mmm160) REVERT: H 815 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6988 (pp) REVERT: J 665 ARG cc_start: 0.3099 (mmm160) cc_final: 0.2474 (pmt-80) REVERT: K 738 MET cc_start: 0.8220 (mmm) cc_final: 0.7884 (mpp) REVERT: L 125 ASP cc_start: 0.7610 (m-30) cc_final: 0.7377 (m-30) REVERT: S 151 MET cc_start: -0.1051 (mpp) cc_final: -0.1312 (mtm) REVERT: S 297 MET cc_start: -0.4862 (mmt) cc_final: -0.5242 (mpm) REVERT: S 566 MET cc_start: -0.0812 (mpp) cc_final: -0.1166 (mpt) REVERT: S 576 MET cc_start: -0.5433 (ttt) cc_final: -0.6050 (tmt) REVERT: S 582 MET cc_start: -0.1815 (mmt) cc_final: -0.2025 (mmt) REVERT: S 605 MET cc_start: -0.2354 (ttm) cc_final: -0.3180 (tpt) outliers start: 89 outliers final: 21 residues processed: 1166 average time/residue: 1.6565 time to fit residues: 2535.9465 Evaluate side-chains 703 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 676 time to evaluate : 7.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 712 VAL Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 359 VAL Chi-restraints excluded: chain 7 residue 572 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain B residue 1492 HIS Chi-restraints excluded: chain B residue 2187 CYS Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 584 PHE Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 558 THR Chi-restraints excluded: chain J residue 756 GLN Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain S residue 271 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 818 optimal weight: 3.9990 chunk 734 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 chunk 250 optimal weight: 0.0470 chunk 495 optimal weight: 6.9990 chunk 392 optimal weight: 0.0470 chunk 759 optimal weight: 50.0000 chunk 293 optimal weight: 9.9990 chunk 461 optimal weight: 50.0000 chunk 565 optimal weight: 3.9990 chunk 879 optimal weight: 7.9990 overall best weight: 3.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 294 GLN Q 538 HIS Q 602 GLN 2 257 GLN 3 298 GLN 3 650 GLN 4 588 HIS ** 4 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 525 ASN 5 535 HIS 7 238 GLN 7 290 GLN 7 459 HIS 7 465 GLN 7 542 GLN A 410 GLN C 254 HIS D 20 GLN D 48 ASN D 184 GLN D 188 GLN F 58 ASN G 191 GLN H 542 GLN I 464 ASN I 494 HIS I 736 HIS I 761 GLN I 762 GLN ** J 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN K 175 GLN K 470 ASN O 210 ASN S 641 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 80450 Z= 0.401 Angle : 0.712 15.374 108898 Z= 0.368 Chirality : 0.046 0.266 12204 Planarity : 0.005 0.073 13869 Dihedral : 10.158 157.708 11323 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.42 % Rotamer: Outliers : 2.69 % Allowed : 10.72 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % 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: -0.45 (0.08), residues: 9604 helix: 0.42 (0.08), residues: 4166 sheet: -0.48 (0.14), residues: 1321 loop : -0.88 (0.10), residues: 4117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 676 HIS 0.016 0.001 HIS I 736 PHE 0.033 0.002 PHE I 516 TYR 0.029 0.002 TYR 6 546 ARG 0.011 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 731 time to evaluate : 7.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 268 MET cc_start: 0.7601 (mtm) cc_final: 0.7269 (mtp) REVERT: 3 426 MET cc_start: 0.8467 (mtp) cc_final: 0.8238 (mtp) REVERT: 5 516 MET cc_start: 0.8440 (mtm) cc_final: 0.8219 (mtp) REVERT: 6 334 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.7399 (t-100) REVERT: 6 438 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7510 (mt-10) REVERT: 6 465 MET cc_start: 0.8144 (mtm) cc_final: 0.7866 (mtm) REVERT: 7 205 MET cc_start: 0.8815 (mmm) cc_final: 0.8425 (mmm) REVERT: 7 354 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6229 (mm) REVERT: 7 492 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.5897 (m-80) REVERT: 7 588 MET cc_start: 0.8437 (ttt) cc_final: 0.8083 (ttp) REVERT: 7 636 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8834 (mm) REVERT: B 1632 MET cc_start: 0.5466 (mpp) cc_final: 0.4530 (pmt) REVERT: B 1754 MET cc_start: 0.4099 (mmt) cc_final: 0.3681 (mtt) REVERT: B 1845 MET cc_start: 0.6651 (mmm) cc_final: 0.6202 (mmp) REVERT: B 2086 MET cc_start: 0.5181 (mpt) cc_final: 0.4816 (ppp) REVERT: C 451 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6346 (mtm) REVERT: D 156 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6014 (m-10) REVERT: E 93 MET cc_start: 0.8539 (tpt) cc_final: 0.8263 (tpt) REVERT: F 23 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: F 68 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8561 (pp) REVERT: G 81 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: G 157 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7828 (p0) REVERT: G 190 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: H 584 PHE cc_start: 0.3577 (OUTLIER) cc_final: 0.1437 (t80) REVERT: H 613 ILE cc_start: 0.5085 (mt) cc_final: 0.4268 (mm) REVERT: H 640 TYR cc_start: 0.3865 (p90) cc_final: 0.3633 (p90) REVERT: H 649 MET cc_start: 0.5914 (ppp) cc_final: 0.5615 (pp-130) REVERT: H 777 ARG cc_start: 0.7522 (mtt-85) cc_final: 0.6907 (mmm160) REVERT: H 778 GLU cc_start: 0.5000 (OUTLIER) cc_final: 0.4697 (tm-30) REVERT: H 815 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6597 (pp) REVERT: I 762 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: J 665 ARG cc_start: 0.3311 (mmm160) cc_final: 0.2546 (pmt-80) REVERT: J 788 MET cc_start: 0.3428 (mmt) cc_final: 0.2874 (tpp) REVERT: K 348 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: O 62 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6269 (pp) REVERT: S 566 MET cc_start: -0.1621 (mpp) cc_final: -0.1992 (mpt) REVERT: S 576 MET cc_start: -0.5168 (ttt) cc_final: -0.5865 (tmt) REVERT: S 605 MET cc_start: -0.2140 (ttm) cc_final: -0.3007 (tpt) outliers start: 227 outliers final: 76 residues processed: 888 average time/residue: 1.5764 time to fit residues: 1868.5882 Evaluate side-chains 730 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 637 time to evaluate : 7.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 311 ASN Chi-restraints excluded: chain Q residue 316 ASP Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 712 VAL Chi-restraints excluded: chain 2 residue 741 ASP Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 614 THR Chi-restraints excluded: chain 4 residue 155 THR Chi-restraints excluded: chain 4 residue 376 ASN Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 539 SER Chi-restraints excluded: chain 4 residue 631 ILE Chi-restraints excluded: chain 5 residue 110 VAL Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 5 residue 474 ILE Chi-restraints excluded: chain 5 residue 490 SER Chi-restraints excluded: chain 5 residue 498 THR Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 531 MET Chi-restraints excluded: chain 5 residue 555 ASP Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 350 LEU Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 497 THR Chi-restraints excluded: chain 7 residue 4 LYS Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 281 LEU Chi-restraints excluded: chain 7 residue 354 LEU Chi-restraints excluded: chain 7 residue 359 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 492 TYR Chi-restraints excluded: chain 7 residue 636 LEU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain B residue 1492 HIS Chi-restraints excluded: chain B residue 2206 VAL Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 284 TRP Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain H residue 555 ARG Chi-restraints excluded: chain H residue 584 PHE Chi-restraints excluded: chain H residue 778 GLU Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain I residue 443 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 762 GLN Chi-restraints excluded: chain J residue 558 THR Chi-restraints excluded: chain J residue 627 LEU Chi-restraints excluded: chain J residue 756 GLN Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain K residue 175 GLN Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 271 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 489 optimal weight: 20.0000 chunk 273 optimal weight: 0.5980 chunk 732 optimal weight: 50.0000 chunk 599 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 881 optimal weight: 9.9990 chunk 952 optimal weight: 10.0000 chunk 785 optimal weight: 4.9990 chunk 874 optimal weight: 8.9990 chunk 300 optimal weight: 0.8980 chunk 707 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 602 GLN 2 257 GLN 2 427 ASN 2 777 HIS 3 298 GLN 4 633 ASN 4 765 HIS 5 645 GLN 6 171 GLN 6 581 GLN 6 597 GLN D 20 GLN D 184 GLN F 58 ASN G 221 GLN H 542 GLN ** I 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 463 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 80450 Z= 0.298 Angle : 0.638 15.251 108898 Z= 0.328 Chirality : 0.043 0.394 12204 Planarity : 0.004 0.065 13869 Dihedral : 9.738 158.369 11308 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 2.78 % Allowed : 12.26 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % 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: -0.26 (0.08), residues: 9604 helix: 0.63 (0.08), residues: 4145 sheet: -0.44 (0.14), residues: 1339 loop : -0.81 (0.10), residues: 4120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 676 HIS 0.010 0.001 HIS 5 524 PHE 0.021 0.002 PHE I 433 TYR 0.027 0.002 TYR R 18 ARG 0.009 0.000 ARG 3 623 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 687 time to evaluate : 7.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 503 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.6015 (mm-30) REVERT: 3 268 MET cc_start: 0.7570 (mtm) cc_final: 0.7297 (mtp) REVERT: 3 561 LYS cc_start: 0.7199 (mttp) cc_final: 0.5918 (mmtt) REVERT: 5 245 MET cc_start: 0.9077 (tpp) cc_final: 0.8862 (tpt) REVERT: 5 430 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7118 (mt-10) REVERT: 5 434 MET cc_start: 0.8411 (mmm) cc_final: 0.7996 (mtm) REVERT: 6 334 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.7696 (t-100) REVERT: 6 438 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7525 (mt-10) REVERT: 6 465 MET cc_start: 0.8116 (mtm) cc_final: 0.7854 (mtm) REVERT: 7 520 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8472 (mm) REVERT: 7 531 LEU cc_start: 0.8791 (tp) cc_final: 0.8549 (tt) REVERT: 7 636 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8575 (mm) REVERT: B 1845 MET cc_start: 0.6910 (mmm) cc_final: 0.6490 (mmp) REVERT: C 539 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7824 (t-170) REVERT: D 126 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.6865 (tpt-90) REVERT: D 132 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6836 (pt0) REVERT: D 156 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.6322 (m-10) REVERT: E 68 VAL cc_start: 0.8809 (t) cc_final: 0.8566 (m) REVERT: E 93 MET cc_start: 0.8450 (tpt) cc_final: 0.8211 (tpt) REVERT: E 95 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8536 (mm) REVERT: F 23 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: F 68 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8508 (pp) REVERT: G 81 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: G 157 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7863 (p0) REVERT: H 583 LEU cc_start: 0.6288 (pp) cc_final: 0.6007 (tp) REVERT: H 584 PHE cc_start: 0.3580 (OUTLIER) cc_final: 0.1296 (t80) REVERT: H 613 ILE cc_start: 0.4995 (mt) cc_final: 0.4412 (mm) REVERT: H 640 TYR cc_start: 0.3899 (p90) cc_final: 0.3672 (p90) REVERT: H 649 MET cc_start: 0.5732 (ppp) cc_final: 0.5470 (pp-130) REVERT: H 766 MET cc_start: 0.3970 (tpp) cc_final: 0.3624 (mmt) REVERT: H 777 ARG cc_start: 0.7545 (mtt-85) cc_final: 0.6942 (mmm160) REVERT: H 815 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6484 (pp) REVERT: I 788 MET cc_start: 0.4459 (ttt) cc_final: 0.3539 (tmm) REVERT: J 788 MET cc_start: 0.3377 (OUTLIER) cc_final: 0.2714 (tpp) REVERT: K 252 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7210 (tp30) REVERT: K 348 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: K 738 MET cc_start: 0.8184 (mmm) cc_final: 0.7887 (mpp) REVERT: L 89 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7255 (mtmt) REVERT: L 126 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7528 (tpt170) REVERT: R 17 MET cc_start: 0.4466 (pmm) cc_final: 0.4170 (ppp) REVERT: R 18 TYR cc_start: 0.1681 (OUTLIER) cc_final: 0.1023 (t80) REVERT: S 151 MET cc_start: -0.1938 (mpt) cc_final: -0.2210 (mpt) REVERT: S 451 MET cc_start: 0.1687 (OUTLIER) cc_final: 0.1113 (mmp) REVERT: S 566 MET cc_start: -0.1387 (mpp) cc_final: -0.1780 (mpt) REVERT: S 576 MET cc_start: -0.5129 (ttt) cc_final: -0.5867 (tmt) REVERT: S 605 MET cc_start: -0.1984 (ttm) cc_final: -0.2708 (tpt) REVERT: S 688 MET cc_start: -0.4032 (mpt) cc_final: -0.4303 (mpt) outliers start: 235 outliers final: 101 residues processed: 855 average time/residue: 1.5705 time to fit residues: 1800.4838 Evaluate side-chains 751 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 629 time to evaluate : 7.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 292 GLU Chi-restraints excluded: chain Q residue 311 ASN Chi-restraints excluded: chain Q residue 316 ASP Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 453 VAL Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 503 GLU Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 712 VAL Chi-restraints excluded: chain 2 residue 741 ASP Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 292 THR Chi-restraints excluded: chain 4 residue 376 ASN Chi-restraints excluded: chain 4 residue 382 VAL Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 539 SER Chi-restraints excluded: chain 4 residue 579 MET Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 5 residue 30 GLN Chi-restraints excluded: chain 5 residue 226 THR Chi-restraints excluded: chain 5 residue 227 LEU Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 5 residue 474 ILE Chi-restraints excluded: chain 5 residue 490 SER Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 531 MET Chi-restraints excluded: chain 5 residue 555 ASP Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 289 VAL Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 497 THR Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 597 GLN Chi-restraints excluded: chain 7 residue 4 LYS Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 281 LEU Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 359 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 636 LEU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain B residue 1492 HIS Chi-restraints excluded: chain B residue 1715 GLU Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain B residue 2206 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 555 ARG Chi-restraints excluded: chain H residue 584 PHE Chi-restraints excluded: chain H residue 680 ILE Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain J residue 558 THR Chi-restraints excluded: chain J residue 627 LEU Chi-restraints excluded: chain J residue 756 GLN Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain K residue 493 CYS Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 271 VAL Chi-restraints excluded: chain S residue 451 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 870 optimal weight: 8.9990 chunk 662 optimal weight: 8.9990 chunk 457 optimal weight: 50.0000 chunk 97 optimal weight: 2.9990 chunk 420 optimal weight: 0.8980 chunk 591 optimal weight: 0.9990 chunk 884 optimal weight: 1.9990 chunk 936 optimal weight: 0.9990 chunk 462 optimal weight: 50.0000 chunk 838 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 602 GLN 2 257 GLN 3 298 GLN 3 584 GLN 4 559 GLN 5 645 GLN B1448 ASN C 364 HIS D 20 GLN D 48 ASN D 184 GLN F 58 ASN G 191 GLN H 542 GLN H 794 ASN ** I 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN O 188 HIS O 208 ASN ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN S 109 ASN S 156 GLN S 193 GLN S 641 ASN T 80 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 80450 Z= 0.246 Angle : 0.603 14.116 108898 Z= 0.309 Chirality : 0.042 0.220 12204 Planarity : 0.004 0.061 13869 Dihedral : 9.488 158.374 11307 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.42 % Rotamer: Outliers : 3.07 % Allowed : 12.75 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % 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: -0.10 (0.09), residues: 9604 helix: 0.81 (0.08), residues: 4141 sheet: -0.40 (0.14), residues: 1349 loop : -0.77 (0.10), residues: 4114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 676 HIS 0.016 0.001 HIS I 736 PHE 0.041 0.002 PHE 6 593 TYR 0.026 0.001 TYR R 18 ARG 0.010 0.000 ARG 3 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 686 time to evaluate : 7.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 503 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5999 (mm-30) REVERT: 3 268 MET cc_start: 0.7563 (mtm) cc_final: 0.7266 (mtp) REVERT: 3 426 MET cc_start: 0.8312 (mtp) cc_final: 0.8077 (mtp) REVERT: 3 561 LYS cc_start: 0.7182 (mttp) cc_final: 0.5882 (mmtt) REVERT: 4 708 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8627 (mp10) REVERT: 5 245 MET cc_start: 0.9073 (tpp) cc_final: 0.8869 (tpt) REVERT: 5 430 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7080 (mt-10) REVERT: 6 438 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7468 (mt-10) REVERT: 6 465 MET cc_start: 0.8132 (mtm) cc_final: 0.7859 (mtm) REVERT: 6 652 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8328 (mt) REVERT: 7 102 TYR cc_start: 0.6371 (t80) cc_final: 0.6080 (t80) REVERT: 7 531 LEU cc_start: 0.8801 (tp) cc_final: 0.8569 (tt) REVERT: 7 636 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8228 (mm) REVERT: B 1754 MET cc_start: 0.3407 (mtt) cc_final: 0.2963 (mtt) REVERT: B 1798 MET cc_start: -0.0712 (mmp) cc_final: -0.3194 (mtt) REVERT: B 1845 MET cc_start: 0.6739 (mmm) cc_final: 0.6327 (mmp) REVERT: B 2241 ASP cc_start: 0.7964 (m-30) cc_final: 0.7609 (m-30) REVERT: C 539 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7816 (t-170) REVERT: D 126 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.6710 (tpt-90) REVERT: D 156 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.6268 (m-10) REVERT: E 95 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8541 (mm) REVERT: F 23 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: F 68 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8481 (pp) REVERT: F 111 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8107 (mptt) REVERT: G 81 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7107 (tt0) REVERT: G 157 ASP cc_start: 0.8176 (p0) cc_final: 0.7865 (p0) REVERT: H 583 LEU cc_start: 0.6208 (pp) cc_final: 0.5992 (tp) REVERT: H 603 LEU cc_start: 0.2710 (OUTLIER) cc_final: 0.2490 (tt) REVERT: H 613 ILE cc_start: 0.5875 (mt) cc_final: 0.5617 (mm) REVERT: H 640 TYR cc_start: 0.3944 (p90) cc_final: 0.3711 (p90) REVERT: H 649 MET cc_start: 0.5716 (ppp) cc_final: 0.5480 (pp-130) REVERT: H 766 MET cc_start: 0.3888 (tpp) cc_final: 0.3570 (mmt) REVERT: H 777 ARG cc_start: 0.7542 (mtt-85) cc_final: 0.6970 (mmm160) REVERT: H 815 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6526 (pp) REVERT: J 736 HIS cc_start: 0.6335 (p90) cc_final: 0.6093 (p90) REVERT: J 788 MET cc_start: 0.3486 (OUTLIER) cc_final: 0.2846 (tpp) REVERT: K 11 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8075 (mp) REVERT: K 252 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: K 491 GLU cc_start: 0.6994 (tp30) cc_final: 0.6680 (tp30) REVERT: K 738 MET cc_start: 0.8173 (mmm) cc_final: 0.7849 (mpp) REVERT: L 89 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7258 (mtmt) REVERT: L 126 ARG cc_start: 0.7630 (tpp80) cc_final: 0.7394 (tpt170) REVERT: O 62 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6219 (pp) REVERT: O 173 MET cc_start: 0.7535 (pmm) cc_final: 0.7286 (pmm) REVERT: R 17 MET cc_start: 0.4371 (pmm) cc_final: 0.4084 (ppp) REVERT: S 151 MET cc_start: -0.1690 (mpt) cc_final: -0.2140 (mpt) REVERT: S 566 MET cc_start: -0.1535 (mpp) cc_final: -0.1936 (mpt) REVERT: S 576 MET cc_start: -0.5262 (ttt) cc_final: -0.5990 (OUTLIER) REVERT: S 605 MET cc_start: -0.2016 (ttm) cc_final: -0.2794 (tpt) REVERT: S 688 MET cc_start: -0.4186 (mpt) cc_final: -0.4606 (mpt) outliers start: 260 outliers final: 106 residues processed: 877 average time/residue: 1.5392 time to fit residues: 1822.9990 Evaluate side-chains 757 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 633 time to evaluate : 7.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 316 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 503 GLU Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 712 VAL Chi-restraints excluded: chain 2 residue 741 ASP Chi-restraints excluded: chain 2 residue 762 ILE Chi-restraints excluded: chain 3 residue 5 VAL Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 227 ASP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 435 LYS Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 614 THR Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 292 THR Chi-restraints excluded: chain 4 residue 382 VAL Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 417 ASP Chi-restraints excluded: chain 4 residue 579 MET Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 4 residue 708 GLN Chi-restraints excluded: chain 5 residue 110 VAL Chi-restraints excluded: chain 5 residue 227 LEU Chi-restraints excluded: chain 5 residue 234 ASP Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 5 residue 442 VAL Chi-restraints excluded: chain 5 residue 474 ILE Chi-restraints excluded: chain 5 residue 490 SER Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 531 MET Chi-restraints excluded: chain 5 residue 555 ASP Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 289 VAL Chi-restraints excluded: chain 6 residue 330 THR Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 497 THR Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 576 LEU Chi-restraints excluded: chain 6 residue 652 LEU Chi-restraints excluded: chain 6 residue 656 ILE Chi-restraints excluded: chain 7 residue 4 LYS Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 281 LEU Chi-restraints excluded: chain 7 residue 359 VAL Chi-restraints excluded: chain 7 residue 403 TYR Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 636 LEU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain B residue 2206 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 555 ARG Chi-restraints excluded: chain H residue 586 VAL Chi-restraints excluded: chain H residue 603 LEU Chi-restraints excluded: chain H residue 647 VAL Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain I residue 443 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 576 MET Chi-restraints excluded: chain J residue 558 THR Chi-restraints excluded: chain J residue 627 LEU Chi-restraints excluded: chain J residue 756 GLN Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain K residue 493 CYS Chi-restraints excluded: chain K residue 692 LEU Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain S residue 271 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 780 optimal weight: 7.9990 chunk 531 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 697 optimal weight: 30.0000 chunk 386 optimal weight: 6.9990 chunk 799 optimal weight: 3.9990 chunk 647 optimal weight: 40.0000 chunk 1 optimal weight: 20.0000 chunk 478 optimal weight: 10.0000 chunk 840 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 602 GLN ** 2 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 584 GLN ** 5 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 645 GLN 6 509 HIS 6 597 GLN 7 504 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1454 HIS B1492 HIS B1901 HIS C 235 GLN C 282 GLN C 364 HIS D 20 GLN D 184 GLN H 542 GLN H 717 GLN I 494 HIS ** I 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 GLN ** J 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 229 GLN L 95 HIS ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 160 GLN ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 80450 Z= 0.546 Angle : 0.720 13.441 108898 Z= 0.367 Chirality : 0.048 0.242 12204 Planarity : 0.005 0.092 13869 Dihedral : 9.732 157.889 11298 Min Nonbonded Distance : 1.555 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 3.33 % Allowed : 13.54 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.08), residues: 9604 helix: 0.58 (0.08), residues: 4144 sheet: -0.56 (0.14), residues: 1350 loop : -0.90 (0.09), residues: 4110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 676 HIS 0.009 0.001 HIS I 736 PHE 0.029 0.002 PHE I 516 TYR 0.028 0.002 TYR 3 32 ARG 0.011 0.001 ARG 3 623 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 673 time to evaluate : 7.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 308 MET cc_start: 0.5087 (tmm) cc_final: 0.4854 (tmm) REVERT: 2 503 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5939 (mm-30) REVERT: 2 770 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6951 (mpp) REVERT: 3 128 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7071 (pp20) REVERT: 3 224 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7760 (p0) REVERT: 3 268 MET cc_start: 0.7505 (mtm) cc_final: 0.7194 (mtp) REVERT: 3 426 MET cc_start: 0.8527 (mtp) cc_final: 0.8316 (mtp) REVERT: 3 561 LYS cc_start: 0.7196 (mttp) cc_final: 0.5831 (mmtt) REVERT: 5 245 MET cc_start: 0.9084 (tpp) cc_final: 0.8866 (tpt) REVERT: 5 430 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7254 (mt-10) REVERT: 6 438 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7473 (mt-10) REVERT: 6 465 MET cc_start: 0.8152 (mtm) cc_final: 0.7939 (mtm) REVERT: 6 577 LEU cc_start: 0.9091 (tp) cc_final: 0.8841 (mm) REVERT: 7 102 TYR cc_start: 0.6422 (t80) cc_final: 0.6203 (t80) REVERT: 7 195 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8918 (mt) REVERT: 7 205 MET cc_start: 0.8880 (mmm) cc_final: 0.8479 (mmm) REVERT: 7 636 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 1798 MET cc_start: -0.0557 (mmp) cc_final: -0.3021 (mtt) REVERT: B 1845 MET cc_start: 0.6718 (mmm) cc_final: 0.6330 (mmp) REVERT: B 2064 PHE cc_start: 0.6477 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: C 539 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7932 (t-170) REVERT: D 126 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7897 (tpt-90) REVERT: D 156 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: E 112 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: F 68 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8512 (pp) REVERT: F 111 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8175 (mptt) REVERT: F 127 ASP cc_start: 0.7666 (t0) cc_final: 0.7461 (t0) REVERT: G 81 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: G 157 ASP cc_start: 0.8356 (p0) cc_final: 0.8108 (p0) REVERT: H 447 MET cc_start: 0.3223 (tpp) cc_final: 0.2849 (tpp) REVERT: H 583 LEU cc_start: 0.6311 (pp) cc_final: 0.6061 (tp) REVERT: H 584 PHE cc_start: 0.3916 (OUTLIER) cc_final: 0.1655 (t80) REVERT: H 603 LEU cc_start: 0.2560 (OUTLIER) cc_final: 0.2356 (tt) REVERT: H 640 TYR cc_start: 0.4083 (p90) cc_final: 0.3805 (p90) REVERT: H 649 MET cc_start: 0.5752 (ppp) cc_final: 0.5409 (pp-130) REVERT: H 766 MET cc_start: 0.3974 (tpp) cc_final: 0.3584 (mmt) REVERT: H 815 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6545 (pp) REVERT: I 642 ASP cc_start: 0.7552 (p0) cc_final: 0.7285 (p0) REVERT: J 440 LEU cc_start: 0.7859 (mm) cc_final: 0.7631 (mp) REVERT: J 736 HIS cc_start: 0.6347 (p90) cc_final: 0.6139 (p90) REVERT: J 750 GLU cc_start: -0.3432 (OUTLIER) cc_final: -0.4125 (tp30) REVERT: J 788 MET cc_start: 0.3879 (OUTLIER) cc_final: 0.3225 (tpp) REVERT: K 252 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7333 (tp30) REVERT: K 732 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8087 (mm) REVERT: K 738 MET cc_start: 0.8200 (mmm) cc_final: 0.7925 (mpp) REVERT: L 89 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7362 (mtmt) REVERT: L 126 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7490 (tpt170) REVERT: O 62 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6313 (pp) REVERT: S 146 MET cc_start: -0.0012 (tmm) cc_final: -0.0959 (tmm) REVERT: S 151 MET cc_start: -0.1580 (mpt) cc_final: -0.1901 (mpt) REVERT: S 451 MET cc_start: 0.1472 (mmp) cc_final: 0.1071 (mmp) REVERT: S 566 MET cc_start: -0.1405 (mpp) cc_final: -0.1830 (mpt) REVERT: S 576 MET cc_start: -0.5323 (ttt) cc_final: -0.5910 (OUTLIER) REVERT: S 605 MET cc_start: -0.2136 (ttm) cc_final: -0.3001 (tpt) outliers start: 282 outliers final: 140 residues processed: 883 average time/residue: 1.5558 time to fit residues: 1848.5547 Evaluate side-chains 792 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 630 time to evaluate : 7.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 311 ASN Chi-restraints excluded: chain Q residue 316 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 2 residue 453 VAL Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 503 GLU Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 604 MET Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 712 VAL Chi-restraints excluded: chain 2 residue 741 ASP Chi-restraints excluded: chain 2 residue 770 MET Chi-restraints excluded: chain 3 residue 5 VAL Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 128 GLU Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 224 ASP Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 227 ASP Chi-restraints excluded: chain 3 residue 364 ARG Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 435 LYS Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 614 THR Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 292 THR Chi-restraints excluded: chain 4 residue 376 ASN Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 539 SER Chi-restraints excluded: chain 4 residue 548 MET Chi-restraints excluded: chain 4 residue 579 MET Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 4 residue 682 LEU Chi-restraints excluded: chain 5 residue 30 GLN Chi-restraints excluded: chain 5 residue 52 THR Chi-restraints excluded: chain 5 residue 110 VAL Chi-restraints excluded: chain 5 residue 226 THR Chi-restraints excluded: chain 5 residue 227 LEU Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 5 residue 442 VAL Chi-restraints excluded: chain 5 residue 474 ILE Chi-restraints excluded: chain 5 residue 490 SER Chi-restraints excluded: chain 5 residue 498 THR Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 531 MET Chi-restraints excluded: chain 5 residue 555 ASP Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 330 THR Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 497 THR Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 601 LEU Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 656 ILE Chi-restraints excluded: chain 7 residue 4 LYS Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 195 ILE Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 281 LEU Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 359 VAL Chi-restraints excluded: chain 7 residue 403 TYR Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 573 VAL Chi-restraints excluded: chain 7 residue 636 LEU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain B residue 1492 HIS Chi-restraints excluded: chain B residue 2064 PHE Chi-restraints excluded: chain B residue 2206 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 555 ARG Chi-restraints excluded: chain H residue 584 PHE Chi-restraints excluded: chain H residue 586 VAL Chi-restraints excluded: chain H residue 603 LEU Chi-restraints excluded: chain H residue 647 VAL Chi-restraints excluded: chain H residue 680 ILE Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain I residue 443 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 576 MET Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 630 ILE Chi-restraints excluded: chain J residue 507 LEU Chi-restraints excluded: chain J residue 558 THR Chi-restraints excluded: chain J residue 627 LEU Chi-restraints excluded: chain J residue 750 GLU Chi-restraints excluded: chain J residue 756 GLN Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain K residue 493 CYS Chi-restraints excluded: chain K residue 732 LEU Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 88 VAL Chi-restraints excluded: chain O residue 175 CYS Chi-restraints excluded: chain O residue 258 ASP Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 271 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 315 optimal weight: 3.9990 chunk 843 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 549 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 937 optimal weight: 50.0000 chunk 778 optimal weight: 0.9990 chunk 434 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 310 optimal weight: 0.8980 chunk 492 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 288 GLN Q 602 GLN 2 792 ASN 4 623 GLN 4 765 HIS ** 5 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN C 364 HIS D 20 GLN D 184 GLN G 191 GLN H 542 GLN ** I 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 615 HIS ** I 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN S 641 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 80450 Z= 0.181 Angle : 0.592 11.615 108898 Z= 0.300 Chirality : 0.041 0.238 12204 Planarity : 0.004 0.056 13869 Dihedral : 9.345 159.952 11298 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 2.29 % Allowed : 15.02 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % 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: -0.02 (0.09), residues: 9604 helix: 0.93 (0.08), residues: 4110 sheet: -0.45 (0.13), residues: 1413 loop : -0.74 (0.10), residues: 4081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 676 HIS 0.020 0.001 HIS B1492 PHE 0.020 0.001 PHE K 691 TYR 0.033 0.001 TYR 3 589 ARG 0.011 0.000 ARG 3 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 672 time to evaluate : 7.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 503 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5932 (mm-30) REVERT: 2 798 MET cc_start: 0.7293 (tpp) cc_final: 0.7073 (tpp) REVERT: 3 268 MET cc_start: 0.7455 (mtm) cc_final: 0.7152 (mtp) REVERT: 3 561 LYS cc_start: 0.7242 (mttp) cc_final: 0.5909 (mmtt) REVERT: 5 218 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8179 (mmtp) REVERT: 5 425 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.5793 (tpm-80) REVERT: 6 438 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7503 (mt-10) REVERT: 6 465 MET cc_start: 0.8001 (mtm) cc_final: 0.7767 (mtm) REVERT: 6 577 LEU cc_start: 0.9088 (tp) cc_final: 0.8855 (mm) REVERT: 7 102 TYR cc_start: 0.6315 (t80) cc_final: 0.6087 (t80) REVERT: 7 205 MET cc_start: 0.8874 (mmm) cc_final: 0.8511 (mmm) REVERT: 7 531 LEU cc_start: 0.8827 (tp) cc_final: 0.8590 (tt) REVERT: 7 533 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8708 (tt) REVERT: 7 636 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8679 (mm) REVERT: A 425 ARG cc_start: 0.6145 (mmt180) cc_final: 0.5899 (mmt180) REVERT: B 1649 MET cc_start: 0.6730 (tpp) cc_final: 0.6430 (tmm) REVERT: B 1754 MET cc_start: 0.3400 (mtt) cc_final: 0.2938 (mtt) REVERT: B 1798 MET cc_start: -0.0286 (mmp) cc_final: -0.2709 (mtt) REVERT: B 1845 MET cc_start: 0.6727 (mmm) cc_final: 0.6429 (mmp) REVERT: B 2241 ASP cc_start: 0.7985 (m-30) cc_final: 0.7653 (m-30) REVERT: C 451 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6673 (mtm) REVERT: C 539 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7864 (t-170) REVERT: D 126 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7482 (tpt-90) REVERT: D 156 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.5828 (m-80) REVERT: F 68 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8416 (pp) REVERT: F 111 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8073 (mptt) REVERT: F 127 ASP cc_start: 0.7595 (t0) cc_final: 0.7362 (t0) REVERT: G 160 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7504 (mmm-85) REVERT: H 447 MET cc_start: 0.2905 (tpp) cc_final: 0.2515 (tpp) REVERT: H 640 TYR cc_start: 0.4030 (p90) cc_final: 0.3748 (p90) REVERT: H 766 MET cc_start: 0.3995 (tpp) cc_final: 0.3700 (mmt) REVERT: H 815 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6657 (pp) REVERT: I 680 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7207 (mt) REVERT: J 736 HIS cc_start: 0.6353 (p90) cc_final: 0.6139 (p90) REVERT: J 750 GLU cc_start: -0.3414 (OUTLIER) cc_final: -0.4115 (tp30) REVERT: J 788 MET cc_start: 0.3755 (OUTLIER) cc_final: 0.3031 (tpp) REVERT: K 252 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: K 348 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: L 126 ARG cc_start: 0.7630 (tpp80) cc_final: 0.7345 (tpt170) REVERT: O 62 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6275 (pp) REVERT: R 17 MET cc_start: 0.3845 (pmm) cc_final: 0.3450 (ppp) REVERT: S 151 MET cc_start: -0.1781 (mpt) cc_final: -0.2035 (mpt) REVERT: S 566 MET cc_start: -0.1627 (mpp) cc_final: -0.2064 (mpt) REVERT: S 576 MET cc_start: -0.5201 (ttt) cc_final: -0.5784 (OUTLIER) REVERT: S 605 MET cc_start: -0.2142 (ttm) cc_final: -0.3018 (tpt) outliers start: 193 outliers final: 97 residues processed: 826 average time/residue: 1.6008 time to fit residues: 1766.8487 Evaluate side-chains 748 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 634 time to evaluate : 7.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 316 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 2 residue 453 VAL Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 503 GLU Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 642 THR Chi-restraints excluded: chain 2 residue 712 VAL Chi-restraints excluded: chain 2 residue 741 ASP Chi-restraints excluded: chain 2 residue 762 ILE Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 364 ARG Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 614 THR Chi-restraints excluded: chain 3 residue 636 THR Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 292 THR Chi-restraints excluded: chain 4 residue 539 SER Chi-restraints excluded: chain 4 residue 579 MET Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 5 residue 218 LYS Chi-restraints excluded: chain 5 residue 226 THR Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 5 residue 425 ARG Chi-restraints excluded: chain 5 residue 442 VAL Chi-restraints excluded: chain 5 residue 490 SER Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 289 VAL Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 497 THR Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 576 LEU Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 656 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 281 LEU Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 403 TYR Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 533 LEU Chi-restraints excluded: chain 7 residue 573 VAL Chi-restraints excluded: chain 7 residue 636 LEU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain B residue 2102 LEU Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain B residue 2206 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 555 ARG Chi-restraints excluded: chain H residue 586 VAL Chi-restraints excluded: chain H residue 647 VAL Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain I residue 443 THR Chi-restraints excluded: chain I residue 576 MET Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 680 ILE Chi-restraints excluded: chain J residue 558 THR Chi-restraints excluded: chain J residue 627 LEU Chi-restraints excluded: chain J residue 750 GLU Chi-restraints excluded: chain J residue 756 GLN Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 374 MET Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 271 VAL Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 903 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 534 optimal weight: 1.9990 chunk 684 optimal weight: 5.9990 chunk 530 optimal weight: 0.8980 chunk 789 optimal weight: 0.8980 chunk 523 optimal weight: 3.9990 chunk 933 optimal weight: 20.0000 chunk 584 optimal weight: 1.9990 chunk 569 optimal weight: 0.0670 chunk 431 optimal weight: 30.0000 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 602 GLN 3 298 GLN 4 281 GLN 4 376 ASN 4 623 GLN ** 5 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 509 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS D 20 GLN D 48 ASN D 184 GLN ** I 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 641 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 80450 Z= 0.209 Angle : 0.597 14.535 108898 Z= 0.301 Chirality : 0.041 0.276 12204 Planarity : 0.004 0.050 13869 Dihedral : 9.224 159.992 11297 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 2.26 % Allowed : 15.47 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % 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: 0.08 (0.09), residues: 9604 helix: 1.03 (0.08), residues: 4110 sheet: -0.43 (0.13), residues: 1419 loop : -0.71 (0.10), residues: 4075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 676 HIS 0.015 0.001 HIS S 73 PHE 0.023 0.001 PHE 2 824 TYR 0.041 0.001 TYR R 18 ARG 0.012 0.000 ARG 3 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 678 time to evaluate : 7.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 798 MET cc_start: 0.7357 (tpp) cc_final: 0.7102 (tpp) REVERT: 3 128 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: 3 268 MET cc_start: 0.7423 (mtm) cc_final: 0.7136 (mtp) REVERT: 3 561 LYS cc_start: 0.7238 (mttp) cc_final: 0.5897 (mmtt) REVERT: 5 218 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8167 (mmtp) REVERT: 5 425 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5985 (tpm-80) REVERT: 6 465 MET cc_start: 0.7993 (mtm) cc_final: 0.7763 (mtm) REVERT: 6 577 LEU cc_start: 0.9138 (tp) cc_final: 0.8852 (mm) REVERT: 7 205 MET cc_start: 0.8828 (mmm) cc_final: 0.8458 (mmm) REVERT: 7 235 MET cc_start: 0.8326 (ptp) cc_final: 0.8091 (ptp) REVERT: 7 636 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8568 (mm) REVERT: A 425 ARG cc_start: 0.6439 (mmt180) cc_final: 0.6198 (mmt180) REVERT: B 1754 MET cc_start: 0.3200 (mtt) cc_final: 0.2927 (mtt) REVERT: B 1798 MET cc_start: -0.0017 (mmp) cc_final: -0.2639 (mtm) REVERT: B 1845 MET cc_start: 0.6690 (mmm) cc_final: 0.6406 (mmp) REVERT: B 2241 ASP cc_start: 0.7954 (m-30) cc_final: 0.7659 (m-30) REVERT: C 451 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6778 (mtm) REVERT: C 539 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7899 (t-170) REVERT: D 126 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7499 (tpt-90) REVERT: D 156 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: F 23 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: F 68 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8394 (pp) REVERT: F 127 ASP cc_start: 0.7622 (t0) cc_final: 0.7396 (t0) REVERT: H 447 MET cc_start: 0.2682 (tpp) cc_final: 0.2345 (tpp) REVERT: H 584 PHE cc_start: 0.3957 (OUTLIER) cc_final: 0.2009 (t80) REVERT: H 640 TYR cc_start: 0.4028 (p90) cc_final: 0.3762 (p90) REVERT: H 766 MET cc_start: 0.3992 (tpp) cc_final: 0.3696 (mmt) REVERT: H 815 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6710 (pp) REVERT: I 680 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7247 (mt) REVERT: J 447 MET cc_start: 0.5800 (mmm) cc_final: 0.5484 (mmm) REVERT: J 750 GLU cc_start: -0.3413 (OUTLIER) cc_final: -0.4116 (tp30) REVERT: J 788 MET cc_start: 0.3599 (OUTLIER) cc_final: 0.2893 (tpp) REVERT: K 252 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: L 126 ARG cc_start: 0.7648 (tpp80) cc_final: 0.7386 (tpt170) REVERT: O 62 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6197 (pp) REVERT: R 17 MET cc_start: 0.3755 (pmm) cc_final: 0.3470 (ppp) REVERT: S 146 MET cc_start: -0.0089 (tmm) cc_final: -0.1160 (tmm) REVERT: S 151 MET cc_start: -0.1774 (mpt) cc_final: -0.2140 (mpt) REVERT: S 576 MET cc_start: -0.5099 (ttt) cc_final: -0.5723 (OUTLIER) REVERT: S 605 MET cc_start: -0.2115 (ttm) cc_final: -0.3032 (tpt) outliers start: 191 outliers final: 104 residues processed: 824 average time/residue: 1.5999 time to fit residues: 1765.2932 Evaluate side-chains 758 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 638 time to evaluate : 7.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 316 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 2 residue 453 VAL Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 666 THR Chi-restraints excluded: chain 2 residue 712 VAL Chi-restraints excluded: chain 2 residue 741 ASP Chi-restraints excluded: chain 2 residue 762 ILE Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 128 GLU Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 164 THR Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 435 LYS Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 614 THR Chi-restraints excluded: chain 3 residue 636 THR Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 539 SER Chi-restraints excluded: chain 4 residue 579 MET Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 5 residue 218 LYS Chi-restraints excluded: chain 5 residue 226 THR Chi-restraints excluded: chain 5 residue 227 LEU Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 5 residue 425 ARG Chi-restraints excluded: chain 5 residue 442 VAL Chi-restraints excluded: chain 5 residue 474 ILE Chi-restraints excluded: chain 5 residue 490 SER Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 289 VAL Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 497 THR Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 576 LEU Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 358 LEU Chi-restraints excluded: chain 7 residue 359 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 573 VAL Chi-restraints excluded: chain 7 residue 636 LEU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain B residue 2102 LEU Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain B residue 2206 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 555 ARG Chi-restraints excluded: chain H residue 584 PHE Chi-restraints excluded: chain H residue 586 VAL Chi-restraints excluded: chain H residue 647 VAL Chi-restraints excluded: chain H residue 690 ILE Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain I residue 443 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 576 MET Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 680 ILE Chi-restraints excluded: chain J residue 558 THR Chi-restraints excluded: chain J residue 627 LEU Chi-restraints excluded: chain J residue 750 GLU Chi-restraints excluded: chain J residue 756 GLN Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 258 ASP Chi-restraints excluded: chain O residue 374 MET Chi-restraints excluded: chain S residue 271 VAL Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 577 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 chunk 557 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 593 optimal weight: 2.9990 chunk 636 optimal weight: 3.9990 chunk 461 optimal weight: 50.0000 chunk 87 optimal weight: 0.7980 chunk 734 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 602 GLN 4 376 ASN 4 623 GLN ** 4 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 509 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS D 20 GLN D 48 ASN D 184 GLN G 191 GLN H 471 HIS H 542 GLN ** I 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 459 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 80450 Z= 0.260 Angle : 0.619 12.487 108898 Z= 0.311 Chirality : 0.042 0.306 12204 Planarity : 0.004 0.052 13869 Dihedral : 9.235 160.081 11297 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.56 % Favored : 95.38 % Rotamer: Outliers : 2.24 % Allowed : 15.77 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % 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: 0.08 (0.09), residues: 9604 helix: 1.03 (0.08), residues: 4105 sheet: -0.43 (0.13), residues: 1429 loop : -0.70 (0.10), residues: 4070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 676 HIS 0.010 0.001 HIS S 73 PHE 0.021 0.001 PHE G 159 TYR 0.032 0.001 TYR R 18 ARG 0.013 0.000 ARG O 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 657 time to evaluate : 7.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 128 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: 3 268 MET cc_start: 0.7445 (mtm) cc_final: 0.7176 (mtp) REVERT: 3 561 LYS cc_start: 0.7243 (mttp) cc_final: 0.5901 (mmtt) REVERT: 5 319 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: 6 465 MET cc_start: 0.7991 (mtm) cc_final: 0.7778 (mtm) REVERT: 6 577 LEU cc_start: 0.9115 (tp) cc_final: 0.8829 (mm) REVERT: 7 205 MET cc_start: 0.8843 (mmm) cc_final: 0.8489 (mmm) REVERT: 7 235 MET cc_start: 0.8303 (ptp) cc_final: 0.8085 (ptp) REVERT: 7 531 LEU cc_start: 0.8826 (tp) cc_final: 0.8582 (tt) REVERT: 7 636 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8585 (mm) REVERT: B 1754 MET cc_start: 0.3231 (mtt) cc_final: 0.2983 (mtt) REVERT: B 1798 MET cc_start: 0.0353 (mmp) cc_final: -0.2376 (mtt) REVERT: B 1845 MET cc_start: 0.6568 (mmm) cc_final: 0.6297 (mmp) REVERT: B 2241 ASP cc_start: 0.7974 (m-30) cc_final: 0.7674 (m-30) REVERT: C 451 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6814 (mtm) REVERT: C 539 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7878 (t-170) REVERT: D 126 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7521 (tpt-90) REVERT: D 156 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: E 95 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8536 (mm) REVERT: F 23 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: F 68 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8414 (pp) REVERT: G 81 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: H 447 MET cc_start: 0.2633 (tpp) cc_final: 0.2286 (tpp) REVERT: H 584 PHE cc_start: 0.3838 (OUTLIER) cc_final: 0.1931 (t80) REVERT: H 640 TYR cc_start: 0.3945 (p90) cc_final: 0.3732 (p90) REVERT: H 766 MET cc_start: 0.3984 (tpp) cc_final: 0.3688 (mmt) REVERT: H 815 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6829 (pp) REVERT: I 524 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: I 680 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7343 (mt) REVERT: J 447 MET cc_start: 0.5817 (mmm) cc_final: 0.5531 (mmm) REVERT: J 649 MET cc_start: 0.6724 (tmm) cc_final: 0.6090 (tmm) REVERT: J 736 HIS cc_start: 0.6308 (p90) cc_final: 0.6042 (p90) REVERT: J 750 GLU cc_start: -0.3404 (OUTLIER) cc_final: -0.4106 (tp30) REVERT: J 788 MET cc_start: 0.3607 (OUTLIER) cc_final: 0.2894 (tpp) REVERT: K 252 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: L 89 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7084 (mtmt) REVERT: L 126 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7386 (tpt170) REVERT: L 142 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7847 (ttt90) REVERT: O 62 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6113 (pp) REVERT: R 17 MET cc_start: 0.4020 (pmm) cc_final: 0.3742 (ppp) REVERT: R 18 TYR cc_start: 0.0842 (OUTLIER) cc_final: 0.0452 (t80) REVERT: S 146 MET cc_start: -0.0214 (tmm) cc_final: -0.0916 (tmm) REVERT: S 151 MET cc_start: -0.2015 (mpt) cc_final: -0.2318 (mpt) REVERT: S 576 MET cc_start: -0.4855 (ttt) cc_final: -0.5577 (OUTLIER) REVERT: S 605 MET cc_start: -0.2094 (ttm) cc_final: -0.3039 (tpt) outliers start: 189 outliers final: 113 residues processed: 801 average time/residue: 1.5942 time to fit residues: 1708.0235 Evaluate side-chains 765 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 631 time to evaluate : 7.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 316 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 2 residue 453 VAL Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 565 VAL Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 642 THR Chi-restraints excluded: chain 2 residue 666 THR Chi-restraints excluded: chain 2 residue 741 ASP Chi-restraints excluded: chain 2 residue 762 ILE Chi-restraints excluded: chain 3 residue 5 VAL Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 128 GLU Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 364 ARG Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 614 THR Chi-restraints excluded: chain 3 residue 636 THR Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 292 THR Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 539 SER Chi-restraints excluded: chain 4 residue 579 MET Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 4 residue 699 MET Chi-restraints excluded: chain 5 residue 226 THR Chi-restraints excluded: chain 5 residue 227 LEU Chi-restraints excluded: chain 5 residue 319 GLU Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 5 residue 442 VAL Chi-restraints excluded: chain 5 residue 474 ILE Chi-restraints excluded: chain 5 residue 490 SER Chi-restraints excluded: chain 5 residue 498 THR Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 550 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 497 THR Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 576 LEU Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 573 VAL Chi-restraints excluded: chain 7 residue 636 LEU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain B residue 2102 LEU Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain B residue 2206 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 555 ARG Chi-restraints excluded: chain H residue 584 PHE Chi-restraints excluded: chain H residue 586 VAL Chi-restraints excluded: chain H residue 647 VAL Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain I residue 443 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 524 GLU Chi-restraints excluded: chain I residue 576 MET Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 680 ILE Chi-restraints excluded: chain J residue 507 LEU Chi-restraints excluded: chain J residue 558 THR Chi-restraints excluded: chain J residue 627 LEU Chi-restraints excluded: chain J residue 750 GLU Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 175 CYS Chi-restraints excluded: chain O residue 258 ASP Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain S residue 271 VAL Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 849 optimal weight: 30.0000 chunk 894 optimal weight: 7.9990 chunk 816 optimal weight: 0.9990 chunk 870 optimal weight: 7.9990 chunk 523 optimal weight: 7.9990 chunk 379 optimal weight: 7.9990 chunk 683 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 786 optimal weight: 0.0980 chunk 823 optimal weight: 0.9990 chunk 867 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 602 GLN 4 376 ASN ** 4 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 509 HIS 6 597 GLN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1659 ASN C 364 HIS D 20 GLN D 48 ASN D 184 GLN ** I 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 736 HIS ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 80450 Z= 0.225 Angle : 0.612 11.911 108898 Z= 0.308 Chirality : 0.041 0.313 12204 Planarity : 0.004 0.055 13869 Dihedral : 9.161 160.810 11293 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.37 % Rotamer: Outliers : 2.14 % Allowed : 16.01 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % 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: 0.10 (0.09), residues: 9604 helix: 1.06 (0.08), residues: 4115 sheet: -0.43 (0.13), residues: 1443 loop : -0.70 (0.10), residues: 4046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 676 HIS 0.009 0.001 HIS 6 509 PHE 0.024 0.001 PHE 2 824 TYR 0.030 0.001 TYR R 18 ARG 0.014 0.000 ARG 3 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 651 time to evaluate : 8.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 503 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5925 (mm-30) REVERT: 3 128 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: 3 268 MET cc_start: 0.7427 (mtm) cc_final: 0.7154 (mtp) REVERT: 3 561 LYS cc_start: 0.7228 (mttp) cc_final: 0.5914 (mttt) REVERT: 5 319 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: 6 465 MET cc_start: 0.7991 (mtm) cc_final: 0.7753 (mtm) REVERT: 6 577 LEU cc_start: 0.9117 (tp) cc_final: 0.8839 (mm) REVERT: 7 205 MET cc_start: 0.8825 (mmm) cc_final: 0.8478 (mmm) REVERT: 7 235 MET cc_start: 0.8284 (ptp) cc_final: 0.8061 (ptp) REVERT: 7 636 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8501 (mm) REVERT: B 1798 MET cc_start: 0.0581 (mmp) cc_final: -0.2112 (mtt) REVERT: B 1845 MET cc_start: 0.6427 (mmm) cc_final: 0.6166 (mmp) REVERT: B 2063 PHE cc_start: 0.7065 (m-10) cc_final: 0.6840 (m-80) REVERT: B 2201 MET cc_start: 0.6959 (ppp) cc_final: 0.6565 (tmm) REVERT: B 2241 ASP cc_start: 0.7904 (m-30) cc_final: 0.7638 (m-30) REVERT: C 539 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7864 (t-170) REVERT: D 126 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7536 (tpt-90) REVERT: D 156 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.6040 (m-80) REVERT: F 23 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: F 68 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8387 (pp) REVERT: G 81 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: H 447 MET cc_start: 0.2529 (tpp) cc_final: 0.2266 (tpp) REVERT: H 584 PHE cc_start: 0.3787 (OUTLIER) cc_final: 0.1367 (t80) REVERT: H 586 VAL cc_start: 0.7212 (OUTLIER) cc_final: 0.6978 (m) REVERT: H 766 MET cc_start: 0.3987 (tpp) cc_final: 0.3613 (mmt) REVERT: H 815 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6766 (pp) REVERT: I 524 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6654 (pm20) REVERT: I 680 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7330 (mt) REVERT: J 447 MET cc_start: 0.6002 (mmm) cc_final: 0.5734 (mmm) REVERT: J 649 MET cc_start: 0.6885 (tmm) cc_final: 0.6335 (tmm) REVERT: J 736 HIS cc_start: 0.6365 (p90) cc_final: 0.6109 (p90) REVERT: J 750 GLU cc_start: -0.3502 (OUTLIER) cc_final: -0.4173 (tp30) REVERT: J 788 MET cc_start: 0.3551 (OUTLIER) cc_final: 0.2984 (tpp) REVERT: K 252 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: K 738 MET cc_start: 0.8094 (mmm) cc_final: 0.7812 (mtp) REVERT: L 89 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7108 (mtmt) REVERT: L 126 ARG cc_start: 0.7646 (tpp80) cc_final: 0.7391 (tpt170) REVERT: L 142 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7829 (ttt90) REVERT: O 62 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6111 (pp) REVERT: R 17 MET cc_start: 0.4488 (pmm) cc_final: 0.4055 (ppp) REVERT: R 18 TYR cc_start: 0.0867 (OUTLIER) cc_final: 0.0385 (t80) REVERT: S 146 MET cc_start: -0.0033 (tmm) cc_final: -0.0785 (tmm) REVERT: S 151 MET cc_start: -0.2152 (mpt) cc_final: -0.2454 (mpt) REVERT: S 162 MET cc_start: 0.4072 (ppp) cc_final: 0.3696 (ppp) REVERT: S 576 MET cc_start: -0.4850 (ttt) cc_final: -0.5537 (OUTLIER) REVERT: S 605 MET cc_start: -0.2035 (ttm) cc_final: -0.2984 (tpt) outliers start: 181 outliers final: 116 residues processed: 791 average time/residue: 1.6099 time to fit residues: 1708.4233 Evaluate side-chains 764 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 627 time to evaluate : 9.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 316 ASP Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 2 residue 453 VAL Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 503 GLU Chi-restraints excluded: chain 2 residue 565 VAL Chi-restraints excluded: chain 2 residue 581 ARG Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 642 THR Chi-restraints excluded: chain 2 residue 666 THR Chi-restraints excluded: chain 2 residue 712 VAL Chi-restraints excluded: chain 2 residue 741 ASP Chi-restraints excluded: chain 2 residue 762 ILE Chi-restraints excluded: chain 3 residue 5 VAL Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 128 GLU Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 614 THR Chi-restraints excluded: chain 3 residue 636 THR Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 292 THR Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 417 ASP Chi-restraints excluded: chain 4 residue 539 SER Chi-restraints excluded: chain 4 residue 579 MET Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 5 residue 226 THR Chi-restraints excluded: chain 5 residue 227 LEU Chi-restraints excluded: chain 5 residue 319 GLU Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 5 residue 442 VAL Chi-restraints excluded: chain 5 residue 474 ILE Chi-restraints excluded: chain 5 residue 490 SER Chi-restraints excluded: chain 5 residue 498 THR Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 550 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 497 THR Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 537 VAL Chi-restraints excluded: chain 6 residue 576 LEU Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 656 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 359 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 573 VAL Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 636 LEU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain B residue 2206 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 584 PHE Chi-restraints excluded: chain H residue 586 VAL Chi-restraints excluded: chain H residue 647 VAL Chi-restraints excluded: chain H residue 680 ILE Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain I residue 443 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 524 GLU Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 680 ILE Chi-restraints excluded: chain J residue 507 LEU Chi-restraints excluded: chain J residue 627 LEU Chi-restraints excluded: chain J residue 750 GLU Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 175 CYS Chi-restraints excluded: chain O residue 212 LEU Chi-restraints excluded: chain O residue 258 ASP Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain S residue 271 VAL Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 571 optimal weight: 0.8980 chunk 920 optimal weight: 40.0000 chunk 561 optimal weight: 0.9990 chunk 436 optimal weight: 20.0000 chunk 639 optimal weight: 1.9990 chunk 965 optimal weight: 9.9990 chunk 888 optimal weight: 3.9990 chunk 768 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 593 optimal weight: 0.9990 chunk 471 optimal weight: 50.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 602 GLN 4 300 GLN 4 623 GLN ** 4 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 765 HIS ** 5 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 494 ASN 6 509 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1901 HIS B2191 GLN D 48 ASN D 184 GLN G 191 GLN ** I 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 641 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 80450 Z= 0.190 Angle : 0.613 14.411 108898 Z= 0.305 Chirality : 0.041 0.305 12204 Planarity : 0.004 0.051 13869 Dihedral : 9.078 161.255 11292 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 1.70 % Allowed : 16.60 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.09), residues: 9604 helix: 1.13 (0.08), residues: 4101 sheet: -0.40 (0.13), residues: 1437 loop : -0.69 (0.10), residues: 4066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 676 HIS 0.009 0.001 HIS 6 509 PHE 0.020 0.001 PHE K 691 TYR 0.028 0.001 TYR R 18 ARG 0.010 0.000 ARG 3 596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19208 Ramachandran restraints generated. 9604 Oldfield, 0 Emsley, 9604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 652 time to evaluate : 7.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 503 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5948 (mm-30) REVERT: 3 128 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: 3 268 MET cc_start: 0.7398 (mtm) cc_final: 0.7116 (mtp) REVERT: 3 561 LYS cc_start: 0.7175 (mttp) cc_final: 0.5872 (mttt) REVERT: 6 465 MET cc_start: 0.8029 (mtm) cc_final: 0.7802 (mtm) REVERT: 6 577 LEU cc_start: 0.9114 (tp) cc_final: 0.8835 (mm) REVERT: 7 205 MET cc_start: 0.8825 (mmm) cc_final: 0.8430 (mmt) REVERT: 7 636 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8306 (mm) REVERT: 7 639 MET cc_start: 0.7717 (pmm) cc_final: 0.7502 (pmm) REVERT: B 1798 MET cc_start: 0.0529 (mmp) cc_final: -0.2156 (mtt) REVERT: B 1845 MET cc_start: 0.6335 (mmm) cc_final: 0.6085 (mmp) REVERT: B 2063 PHE cc_start: 0.7057 (m-10) cc_final: 0.6826 (m-80) REVERT: B 2086 MET cc_start: 0.3071 (pmm) cc_final: 0.2437 (pmm) REVERT: B 2201 MET cc_start: 0.6994 (ppp) cc_final: 0.6724 (tmm) REVERT: B 2241 ASP cc_start: 0.7873 (m-30) cc_final: 0.7617 (m-30) REVERT: C 175 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.7487 (tpp-160) REVERT: C 539 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7883 (t-170) REVERT: D 126 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7532 (tpt-90) REVERT: D 156 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: F 23 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: F 68 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8362 (pp) REVERT: G 81 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: H 447 MET cc_start: 0.2559 (tpp) cc_final: 0.2263 (tpp) REVERT: H 584 PHE cc_start: 0.3735 (OUTLIER) cc_final: 0.1243 (t80) REVERT: H 586 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6962 (m) REVERT: H 601 VAL cc_start: 0.5624 (p) cc_final: 0.4994 (p) REVERT: H 766 MET cc_start: 0.3821 (tpp) cc_final: 0.3491 (mmt) REVERT: H 815 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6818 (pp) REVERT: I 524 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6660 (pm20) REVERT: J 447 MET cc_start: 0.5991 (mmm) cc_final: 0.5731 (mmm) REVERT: J 649 MET cc_start: 0.6846 (tmm) cc_final: 0.6406 (tmm) REVERT: J 736 HIS cc_start: 0.6390 (p90) cc_final: 0.6150 (p90) REVERT: J 750 GLU cc_start: -0.3359 (OUTLIER) cc_final: -0.4405 (tp30) REVERT: J 788 MET cc_start: 0.3495 (OUTLIER) cc_final: 0.2934 (tpp) REVERT: K 252 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: K 738 MET cc_start: 0.8046 (mmm) cc_final: 0.7768 (mtp) REVERT: L 126 ARG cc_start: 0.7622 (tpp80) cc_final: 0.7391 (tpt170) REVERT: L 142 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7767 (ttt90) REVERT: O 62 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6034 (pp) REVERT: R 17 MET cc_start: 0.4161 (pmm) cc_final: 0.3682 (ppp) REVERT: R 18 TYR cc_start: 0.0579 (OUTLIER) cc_final: 0.0196 (t80) REVERT: S 146 MET cc_start: -0.0104 (tmm) cc_final: -0.0864 (tmm) REVERT: S 151 MET cc_start: -0.2255 (mpt) cc_final: -0.2522 (mpt) REVERT: S 162 MET cc_start: 0.4259 (ppp) cc_final: 0.3899 (ppp) REVERT: S 566 MET cc_start: -0.1072 (mmt) cc_final: -0.1515 (mmt) REVERT: S 576 MET cc_start: -0.5160 (ttt) cc_final: -0.5486 (OUTLIER) REVERT: S 605 MET cc_start: -0.2041 (ttm) cc_final: -0.2958 (tpt) outliers start: 143 outliers final: 103 residues processed: 769 average time/residue: 1.6462 time to fit residues: 1691.8696 Evaluate side-chains 754 residues out of total 8607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 633 time to evaluate : 8.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 176 ASP Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 2 residue 453 VAL Chi-restraints excluded: chain 2 residue 457 THR Chi-restraints excluded: chain 2 residue 503 GLU Chi-restraints excluded: chain 2 residue 565 VAL Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 642 THR Chi-restraints excluded: chain 2 residue 666 THR Chi-restraints excluded: chain 2 residue 741 ASP Chi-restraints excluded: chain 2 residue 762 ILE Chi-restraints excluded: chain 3 residue 5 VAL Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 128 GLU Chi-restraints excluded: chain 3 residue 142 VAL Chi-restraints excluded: chain 3 residue 173 VAL Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 364 ARG Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 614 THR Chi-restraints excluded: chain 3 residue 636 THR Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 4 residue 292 THR Chi-restraints excluded: chain 4 residue 390 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 405 VAL Chi-restraints excluded: chain 4 residue 417 ASP Chi-restraints excluded: chain 4 residue 539 SER Chi-restraints excluded: chain 4 residue 579 MET Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 5 residue 226 THR Chi-restraints excluded: chain 5 residue 328 LEU Chi-restraints excluded: chain 5 residue 442 VAL Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 550 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 289 VAL Chi-restraints excluded: chain 6 residue 334 TRP Chi-restraints excluded: chain 6 residue 466 ASP Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 497 THR Chi-restraints excluded: chain 6 residue 520 ILE Chi-restraints excluded: chain 6 residue 576 LEU Chi-restraints excluded: chain 6 residue 637 CYS Chi-restraints excluded: chain 6 residue 656 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 237 MET Chi-restraints excluded: chain 7 residue 359 VAL Chi-restraints excluded: chain 7 residue 476 THR Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 573 VAL Chi-restraints excluded: chain 7 residue 636 LEU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain B residue 2206 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain H residue 584 PHE Chi-restraints excluded: chain H residue 586 VAL Chi-restraints excluded: chain H residue 647 VAL Chi-restraints excluded: chain H residue 815 LEU Chi-restraints excluded: chain I residue 443 THR Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 524 GLU Chi-restraints excluded: chain I residue 525 TRP Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain J residue 507 LEU Chi-restraints excluded: chain J residue 627 LEU Chi-restraints excluded: chain J residue 750 GLU Chi-restraints excluded: chain J residue 766 MET Chi-restraints excluded: chain J residue 788 MET Chi-restraints excluded: chain K residue 252 GLU Chi-restraints excluded: chain K residue 445 GLU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 212 LEU Chi-restraints excluded: chain O residue 258 ASP Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain S residue 271 VAL Chi-restraints excluded: chain T residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 969 random chunks: chunk 610 optimal weight: 0.9990 chunk 818 optimal weight: 6.9990 chunk 235 optimal weight: 0.5980 chunk 708 optimal weight: 30.0000 chunk 113 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 769 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 chunk 790 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 602 GLN 4 623 GLN ** 4 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 765 HIS ** 5 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 509 HIS 7 374 ASN 7 465 GLN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1901 HIS D 20 GLN D 48 ASN D 184 GLN ** I 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 641 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.204611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.156626 restraints weight = 183180.231| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 4.36 r_work: 0.3217 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 80450 Z= 0.200 Angle : 0.612 14.434 108898 Z= 0.305 Chirality : 0.041 0.293 12204 Planarity : 0.004 0.060 13869 Dihedral : 9.029 161.487 11292 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.42 % Rotamer: Outliers : 1.73 % Allowed : 16.74 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.05 % 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: 0.19 (0.09), residues: 9604 helix: 1.18 (0.08), residues: 4089 sheet: -0.40 (0.13), residues: 1432 loop : -0.69 (0.10), residues: 4083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 676 HIS 0.009 0.001 HIS 6 509 PHE 0.021 0.001 PHE J 567 TYR 0.025 0.001 TYR B2008 ARG 0.016 0.000 ARG 7 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28915.47 seconds wall clock time: 502 minutes 47.78 seconds (30167.78 seconds total)