Starting phenix.real_space_refine on Sat Dec 9 10:34:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/12_2023/5oqj_3846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/12_2023/5oqj_3846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/12_2023/5oqj_3846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/12_2023/5oqj_3846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/12_2023/5oqj_3846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oqj_3846/12_2023/5oqj_3846_updated.pdb" } resolution = 4.7 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 16 6.06 5 P 148 5.49 5 Mg 1 5.21 5 S 324 5.16 5 C 39122 2.51 5 N 11155 2.21 5 O 12161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A GLU 1280": "OE1" <-> "OE2" Residue "A GLU 1351": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "B ARG 884": "NH1" <-> "NH2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M ARG 320": "NH1" <-> "NH2" Residue "O ARG 79": "NH1" <-> "NH2" Residue "Q ARG 343": "NH1" <-> "NH2" Residue "Q ARG 398": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 251": "NH1" <-> "NH2" Residue "R ARG 271": "NH1" <-> "NH2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W ARG 108": "NH1" <-> "NH2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "W ARG 174": "NH1" <-> "NH2" Residue "W ARG 193": "NH1" <-> "NH2" Residue "X ARG 197": "NH1" <-> "NH2" Residue "X ARG 276": "NH1" <-> "NH2" Residue "0 GLU 78": "OE1" <-> "OE2" Residue "0 GLU 166": "OE1" <-> "OE2" Residue "0 GLU 220": "OE1" <-> "OE2" Residue "0 GLU 340": "OE1" <-> "OE2" Residue "0 GLU 451": "OE1" <-> "OE2" Residue "0 GLU 578": "OE1" <-> "OE2" Residue "0 TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 30": "NH1" <-> "NH2" Residue "1 ARG 61": "NH1" <-> "NH2" Residue "1 ARG 72": "NH1" <-> "NH2" Residue "1 GLU 79": "OE1" <-> "OE2" Residue "1 ARG 86": "NH1" <-> "NH2" Residue "1 ARG 94": "NH1" <-> "NH2" Residue "1 ARG 110": "NH1" <-> "NH2" Residue "1 ARG 286": "NH1" <-> "NH2" Residue "2 PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 37": "NH1" <-> "NH2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 142": "NH1" <-> "NH2" Residue "7 ARG 380": "NH1" <-> "NH2" Residue "7 GLU 635": "OE1" <-> "OE2" Residue "7 ARG 695": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 62931 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" Number of atoms: 10997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10997 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 9178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9178 Classifications: {'peptide': 1152} Link IDs: {'PTRANS': 51, 'TRANS': 1100} Chain breaks: 7 Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2061 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2175 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 2 Chain: "N" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1533 Classifications: {'DNA': 76} Link IDs: {'rna3p': 75} Chain breaks: 1 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 30 Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "Q" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1144 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1303 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 158 Chain: "T" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1440 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Chain breaks: 1 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 30 Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 757 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'TRANS': 91} Chain breaks: 1 Chain: "V" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 782 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain breaks: 1 Chain: "W" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1825 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 59, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 124 Chain: "X" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1004 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 7, 'TRANS': 152} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "0" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 4844 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 224} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 675} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 812 Unresolved non-hydrogen angles: 1050 Unresolved non-hydrogen dihedrals: 656 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 15, 'TYR:plan': 12, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 6, 'GLU:plan': 28, 'ASP:plan': 11, 'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 484 Chain: "1" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3060 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PTRANS': 12, 'TRANS': 478} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 759 Unresolved non-hydrogen angles: 1041 Unresolved non-hydrogen dihedrals: 520 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'ASN:plan1': 10, 'TYR:plan': 6, 'UNK:plan-1': 170, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 389 Chain: "2" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2160 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 320} Link IDs: {'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 972 Unresolved non-hydrogen angles: 1287 Unresolved non-hydrogen dihedrals: 736 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 13, 'ARG:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 12, 'GLU:plan': 12, 'ASP:plan': 12, 'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 484 Chain: "3" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 860 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 178 Chain: "4" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 1475 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'PTRANS': 9, 'TRANS': 287} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 831 Unresolved non-hydrogen angles: 1079 Unresolved non-hydrogen dihedrals: 657 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 9, 'UNK:plan-1': 38, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'ARG:plan': 8, 'PHE:plan': 11, 'GLU:plan': 17, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 396 Chain: "5" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 498 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "6" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2197 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 556 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 3, 'UNK:plan-1': 44, 'HIS:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 9, 'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 228 Chain: "7" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3148 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 11, 'TRANS': 396} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'UNK:plan-1': 45} Unresolved non-hydrogen planarities: 45 Chain: "Z" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 215 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'TRANS': 42} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "6" 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 813 SG CYS A 107 100.851 117.685 115.078 1.00 0.00 S ATOM 837 SG CYS A 110 100.839 118.916 118.341 1.00 0.00 S ATOM 1142 SG CYS A 148 104.560 118.031 117.299 1.00 0.00 S ATOM 1211 SG CYS A 167 101.990 115.274 117.182 1.00 0.00 S ATOM 508 SG CYS A 67 63.199 143.269 98.435 1.00 0.00 S ATOM 530 SG CYS A 70 65.448 145.824 101.450 1.00 0.00 S ATOM 583 SG CYS A 77 65.905 145.050 97.379 1.00 0.00 S ATOM 19693 SG CYS B1163 75.482 148.202 112.426 1.00 0.00 S ATOM 19711 SG CYS B1166 77.441 144.644 110.627 1.00 0.00 S ATOM 19836 SG CYS B1182 73.676 145.332 110.225 1.00 0.00 S ATOM 19855 SG CYS B1185 75.032 144.963 113.427 1.00 0.00 S ATOM 20822 SG CYS C 86 45.822 183.682 45.846 1.00 0.00 S ATOM 20839 SG CYS C 88 44.819 180.412 46.821 1.00 0.00 S ATOM 20872 SG CYS C 92 44.602 181.557 43.519 1.00 0.00 S ATOM 20895 SG CYS C 95 47.903 180.597 44.039 1.00 0.00 S ATOM 28385 SG CYS I 7 134.353 90.890 59.264 1.00 0.00 S ATOM 28410 SG CYS I 10 131.036 89.020 60.966 1.00 0.00 S ATOM 28576 SG CYS I 29 133.309 92.196 62.560 1.00 0.00 S ATOM 28600 SG CYS I 32 134.356 88.834 62.085 1.00 0.00 S ATOM 28927 SG CYS I 75 138.506 124.939 29.557 1.00 0.00 S ATOM 28949 SG CYS I 78 137.347 123.485 26.073 1.00 0.00 S ATOM 29165 SG CYS I 103 134.500 124.015 27.844 1.00 0.00 S ATOM 29185 SG CYS I 106 137.169 121.064 28.777 1.00 0.00 S ATOM 29330 SG CYS J 7 75.875 169.028 31.922 1.00 0.00 S ATOM 29353 SG CYS J 10 75.836 172.274 30.687 1.00 0.00 S ATOM 29633 SG CYS J 45 79.435 171.564 30.824 1.00 0.00 S ATOM 29639 SG CYS J 46 76.709 170.428 28.459 1.00 0.00 S ATOM 30762 SG CYS L 31 49.649 133.781 41.657 1.00 0.00 S ATOM 30782 SG CYS L 34 47.889 133.859 38.525 1.00 0.00 S ATOM 30886 SG CYS L 48 46.937 132.487 42.581 1.00 0.00 S ATOM 30909 SG CYS L 51 49.227 130.629 40.671 1.00 0.00 S ATOM 31137 SG CYS M 24 49.346 163.558 89.133 1.00 0.00 S ATOM 31159 SG CYS M 27 47.050 164.804 87.543 1.00 0.00 S ATOM 31303 SG CYS M 45 48.295 162.172 85.056 1.00 0.00 S ATOM 31322 SG CYS M 48 49.708 165.933 86.696 1.00 0.00 S ATOM 42521 SG CYS W 124 47.670 139.801 111.049 1.00 0.00 S ATOM 42542 SG CYS W 127 50.260 139.734 108.670 1.00 0.00 S ATOM 42727 SG CYS W 149 49.887 142.961 110.631 1.00 0.00 S ATOM 42747 SG CYS W 152 47.477 141.747 107.484 1.00 0.00 S ATOM 45052 SG CYS 0 115 76.172 92.849 191.353 1.00 0.00 S ATOM 45249 SG CYS 0 156 69.955 91.569 193.435 1.00 0.00 S ATOM 45159 SG CYS 0 133 73.716 96.578 192.038 1.00 0.00 S ATOM 45514 SG CYS 0 191 75.045 93.202 196.095 1.00 0.00 S ATOM 54544 SG CYS 3 13 61.254 123.286 142.461 1.00 0.00 S ATOM 54565 SG CYS 3 16 63.898 122.492 139.168 1.00 0.00 S ATOM 54738 SG CYS 3 39 64.203 125.071 141.144 1.00 0.00 S ATOM 54759 SG CYS 3 42 61.224 125.485 139.440 1.00 0.00 S ATOM 54691 SG CYS 3 34 53.712 128.864 151.091 1.00 0.00 S ATOM 54849 SG CYS 3 54 54.742 126.915 147.774 1.00 0.00 S ATOM 54887 SG CYS 3 59 51.819 126.177 149.902 1.00 0.00 S ATOM 56676 SG CYS 4 289 127.763 47.748 212.149 1.00 0.00 S ATOM 56692 SG CYS 4 292 126.340 50.740 210.783 1.00 0.00 S ATOM 56757 SG CYS 4 305 124.624 49.292 213.346 1.00 0.00 S ATOM 56773 SG CYS 4 308 126.971 51.108 214.053 1.00 0.00 S ATOM 58993 SG CYS 6 349 129.166 31.893 196.025 1.00 0.00 S ATOM 59009 SG CYS 6 352 127.486 29.935 193.728 1.00 0.00 S ATOM 59065 SG CYS 6 363 128.452 33.371 192.846 1.00 0.00 S ATOM 59081 SG CYS 6 366 125.577 32.050 195.758 1.00 0.00 S ATOM 59267 SG CYS 6 403 157.099 66.436 208.131 1.00 0.00 S ATOM 59283 SG CYS 6 406 159.222 65.735 205.423 1.00 0.00 S ATOM 59441 SG CYS 6 437 156.821 68.846 205.444 1.00 0.00 S ATOM 59457 SG CYS 6 440 155.510 65.616 205.017 1.00 0.00 S ATOM 59399 SG CYS 6 429 147.879 64.946 215.027 1.00 0.00 S ATOM 59415 SG CYS 6 432 150.669 63.572 217.144 1.00 0.00 S ATOM 59513 SG CYS 6 451 150.155 62.503 213.931 1.00 0.00 S ATOM 59528 SG CYS 6 454 147.437 61.152 215.961 1.00 0.00 S Time building chain proxies: 25.44, per 1000 atoms: 0.40 Number of scatterers: 62931 At special positions: 0 Unit cell: (217.83, 231.53, 242.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 16 29.99 Fe 4 26.01 S 324 16.00 P 148 15.00 Mg 1 11.99 O 12161 8.00 N 11155 7.00 C 39122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.95 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " Number of angles added : 90 15006 Ramachandran restraints generated. 7503 Oldfield, 0 Emsley, 7503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 308 helices and 77 sheets defined 43.1% alpha, 13.5% beta 69 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 21.71 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 104 removed outlier: 4.594A pdb=" N ALA A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 231 through 234 No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 526 through 534 removed outlier: 3.581A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.906A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.586A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.516A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 660 removed outlier: 3.550A pdb=" N CYS A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 646 " --> pdb=" O CYS A 642 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 761 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.982A pdb=" N PHE A 815 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 890 through 896 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 916 through 919 No H-bonds generated for 'chain 'A' and resid 916 through 919' Processing helix chain 'A' and resid 923 through 946 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.781A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 5.544A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1064 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1144 through 1146 No H-bonds generated for 'chain 'A' and resid 1144 through 1146' Processing helix chain 'A' and resid 1167 through 1174 removed outlier: 3.834A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1223 removed outlier: 7.821A pdb=" N ASN A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASP A1223 " --> pdb=" O THR A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1270 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.537A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1358 removed outlier: 6.794A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1396 through 1402 removed outlier: 4.165A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1414 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1440 Processing helix chain 'A' and resid 1447 through 1450 No H-bonds generated for 'chain 'A' and resid 1447 through 1450' Processing helix chain 'B' and resid 28 through 40 removed outlier: 4.168A pdb=" N ARG B 39 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 65 removed outlier: 4.425A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.872A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 389 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 438 Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 561 removed outlier: 3.585A pdb=" N SER B 559 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TRP B 561 " --> pdb=" O PHE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 605 Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 700 Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.899A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 751 through 755' Processing helix chain 'B' and resid 764 through 775 removed outlier: 4.389A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 787 Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.997A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 928 through 931 No H-bonds generated for 'chain 'B' and resid 928 through 931' Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1024 through 1038 removed outlier: 3.523A pdb=" N CYS B1029 " --> pdb=" O HIS B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1062 removed outlier: 3.699A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1150 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 76 through 79 removed outlier: 3.765A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 79' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 240 through 263 Processing helix chain 'D' and resid 54 through 72 removed outlier: 3.516A pdb=" N ILE D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 133 removed outlier: 3.647A pdb=" N THR D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'E' and resid 4 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 122 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.580A pdb=" N LYS G 23 " --> pdb=" O PRO G 20 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU G 33 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'I' and resid 60 through 64 removed outlier: 4.553A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 60 through 64' Processing helix chain 'J' and resid 15 through 28 removed outlier: 3.816A pdb=" N TRP J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLU J 19 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER J 20 " --> pdb=" O LYS J 17 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU J 22 " --> pdb=" O GLU J 19 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN J 26 " --> pdb=" O ASN J 23 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU J 27 " --> pdb=" O LEU J 24 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP J 28 " --> pdb=" O LEU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 44 through 51 removed outlier: 4.177A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 61 Processing helix chain 'K' and resid 7 through 9 No H-bonds generated for 'chain 'K' and resid 7 through 9' Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.771A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 109 Processing helix chain 'M' and resid 60 through 64 Processing helix chain 'M' and resid 85 through 88 No H-bonds generated for 'chain 'M' and resid 85 through 88' Processing helix chain 'M' and resid 104 through 116 Processing helix chain 'M' and resid 118 through 120 No H-bonds generated for 'chain 'M' and resid 118 through 120' Processing helix chain 'M' and resid 124 through 140 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 166 through 168 No H-bonds generated for 'chain 'M' and resid 166 through 168' Processing helix chain 'M' and resid 170 through 182 Processing helix chain 'M' and resid 189 through 195 Processing helix chain 'M' and resid 201 through 216 Processing helix chain 'M' and resid 236 through 246 Proline residue: M 240 - end of helix Processing helix chain 'M' and resid 250 through 266 Processing helix chain 'M' and resid 274 through 288 Processing helix chain 'M' and resid 294 through 301 removed outlier: 4.116A pdb=" N VAL M 298 " --> pdb=" O THR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 318 removed outlier: 3.790A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 323 removed outlier: 3.627A pdb=" N LEU M 323 " --> pdb=" O ARG M 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 320 through 323' Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 236 Proline residue: O 232 - end of helix Processing helix chain 'Q' and resid 27 through 34 Processing helix chain 'Q' and resid 108 through 113 Processing helix chain 'Q' and resid 339 through 345 Processing helix chain 'Q' and resid 407 through 414 removed outlier: 3.968A pdb=" N ASP Q 414 " --> pdb=" O GLU Q 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 81 Processing helix chain 'R' and resid 234 through 245 removed outlier: 4.199A pdb=" N LYS R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 296 through 309 Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'R' and resid 326 through 336 removed outlier: 3.704A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 28 removed outlier: 4.388A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 46 Processing helix chain 'V' and resid 9 through 12 Processing helix chain 'V' and resid 14 through 28 Processing helix chain 'V' and resid 36 through 54 Processing helix chain 'W' and resid 5 through 20 Processing helix chain 'W' and resid 23 through 34 Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 51 through 63 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 91 through 115 removed outlier: 3.805A pdb=" N ASP W 112 " --> pdb=" O ARG W 108 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP W 114 " --> pdb=" O LYS W 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS W 115 " --> pdb=" O ASP W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 139 Processing helix chain 'W' and resid 162 through 191 removed outlier: 3.515A pdb=" N LYS W 166 " --> pdb=" O LYS W 163 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS W 168 " --> pdb=" O ASN W 165 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN W 169 " --> pdb=" O LYS W 166 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS W 171 " --> pdb=" O LYS W 168 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN W 173 " --> pdb=" O ASP W 170 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG W 174 " --> pdb=" O LYS W 171 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN W 178 " --> pdb=" O LEU W 175 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN W 180 " --> pdb=" O ASP W 177 " (cutoff:3.500A) Proline residue: W 181 - end of helix removed outlier: 3.921A pdb=" N ASP W 190 " --> pdb=" O LYS W 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP W 191 " --> pdb=" O LYS W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 270 through 286 removed outlier: 3.803A pdb=" N UNK W 274 " --> pdb=" O UNK W 270 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK W 275 " --> pdb=" O UNK W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 351 through 372 Processing helix chain 'X' and resid 125 through 138 Processing helix chain 'X' and resid 144 through 150 Processing helix chain 'X' and resid 158 through 165 Processing helix chain 'X' and resid 189 through 199 removed outlier: 3.851A pdb=" N GLN X 199 " --> pdb=" O LEU X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 208 through 213 Processing helix chain 'X' and resid 217 through 223 Processing helix chain 'X' and resid 257 through 264 Processing helix chain 'X' and resid 271 through 281 removed outlier: 3.932A pdb=" N LEU X 274 " --> pdb=" O PHE X 271 " (cutoff:3.500A) Proline residue: X 275 - end of helix removed outlier: 3.817A pdb=" N ASP X 280 " --> pdb=" O LYS X 277 " (cutoff:3.500A) Processing helix chain '0' and resid 19 through 33 removed outlier: 3.611A pdb=" N TYR 0 24 " --> pdb=" O GLU 0 20 " (cutoff:3.500A) Processing helix chain '0' and resid 48 through 62 removed outlier: 4.253A pdb=" N LEU 0 52 " --> pdb=" O LYS 0 48 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU 0 53 " --> pdb=" O THR 0 49 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR 0 56 " --> pdb=" O LEU 0 52 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS 0 62 " --> pdb=" O ALA 0 58 " (cutoff:3.500A) Processing helix chain '0' and resid 76 through 95 Processing helix chain '0' and resid 117 through 119 No H-bonds generated for 'chain '0' and resid 117 through 119' Processing helix chain '0' and resid 129 through 144 Processing helix chain '0' and resid 165 through 173 removed outlier: 4.300A pdb=" N LEU 0 171 " --> pdb=" O VAL 0 167 " (cutoff:3.500A) Proline residue: 0 172 - end of helix Processing helix chain '0' and resid 179 through 188 Processing helix chain '0' and resid 192 through 200 Processing helix chain '0' and resid 210 through 213 No H-bonds generated for 'chain '0' and resid 210 through 213' Processing helix chain '0' and resid 219 through 225 Processing helix chain '0' and resid 240 through 246 Processing helix chain '0' and resid 255 through 276 Processing helix chain '0' and resid 280 through 300 removed outlier: 8.208A pdb=" N UNK 0 294 " --> pdb=" O VAL 0 290 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N UNK 0 295 " --> pdb=" O GLN 0 291 " (cutoff:3.500A) Processing helix chain '0' and resid 312 through 315 No H-bonds generated for 'chain '0' and resid 312 through 315' Processing helix chain '0' and resid 328 through 346 Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 373 through 387 removed outlier: 3.531A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG 0 380 " --> pdb=" O PHE 0 376 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER 0 382 " --> pdb=" O SER 0 378 " (cutoff:3.500A) Processing helix chain '0' and resid 393 through 410 Processing helix chain '0' and resid 442 through 452 Proline residue: 0 448 - end of helix removed outlier: 4.093A pdb=" N GLU 0 451 " --> pdb=" O LYS 0 447 " (cutoff:3.500A) Processing helix chain '0' and resid 468 through 471 No H-bonds generated for 'chain '0' and resid 468 through 471' Processing helix chain '0' and resid 488 through 490 No H-bonds generated for 'chain '0' and resid 488 through 490' Processing helix chain '0' and resid 504 through 509 removed outlier: 4.370A pdb=" N ARG 0 509 " --> pdb=" O ALA 0 505 " (cutoff:3.500A) Processing helix chain '0' and resid 516 through 532 Processing helix chain '0' and resid 544 through 550 Processing helix chain '0' and resid 558 through 562 Processing helix chain '0' and resid 576 through 590 Processing helix chain '0' and resid 633 through 645 Processing helix chain '0' and resid 656 through 669 removed outlier: 3.648A pdb=" N CYS 0 665 " --> pdb=" O HIS 0 661 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 688 Processing helix chain '0' and resid 701 through 722 removed outlier: 3.726A pdb=" N LEU 0 706 " --> pdb=" O SER 0 702 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA 0 713 " --> pdb=" O SER 0 709 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN 0 716 " --> pdb=" O MET 0 712 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN 0 719 " --> pdb=" O SER 0 715 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE 0 720 " --> pdb=" O ASN 0 716 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU 0 721 " --> pdb=" O THR 0 717 " (cutoff:3.500A) Processing helix chain '1' and resid 94 through 120 removed outlier: 3.940A pdb=" N GLN 1 106 " --> pdb=" O MET 1 102 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE 1 107 " --> pdb=" O THR 1 103 " (cutoff:3.500A) Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 Processing helix chain '1' and resid 189 through 199 Processing helix chain '1' and resid 206 through 212 removed outlier: 3.594A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) Processing helix chain '1' and resid 214 through 224 Processing helix chain '1' and resid 230 through 239 removed outlier: 4.414A pdb=" N UNK 1 238 " --> pdb=" O UNK 1 234 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N UNK 1 239 " --> pdb=" O UNK 1 235 " (cutoff:3.500A) Processing helix chain '1' and resid 252 through 262 Processing helix chain '1' and resid 264 through 273 Processing helix chain '1' and resid 280 through 295 removed outlier: 4.039A pdb=" N ARG 1 286 " --> pdb=" O GLU 1 282 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 309 through 329 removed outlier: 4.402A pdb=" N UNK 1 319 " --> pdb=" O UNK 1 315 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N UNK 1 320 " --> pdb=" O UNK 1 316 " (cutoff:3.500A) Processing helix chain '1' and resid 371 through 393 removed outlier: 4.099A pdb=" N UNK 1 390 " --> pdb=" O UNK 1 386 " (cutoff:3.500A) Processing helix chain '1' and resid 467 through 482 Processing helix chain '1' and resid 487 through 489 No H-bonds generated for 'chain '1' and resid 487 through 489' Processing helix chain '1' and resid 495 through 516 removed outlier: 3.560A pdb=" N UNK 1 503 " --> pdb=" O UNK 1 500 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N UNK 1 507 " --> pdb=" O UNK 1 504 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N UNK 1 510 " --> pdb=" O UNK 1 507 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N UNK 1 514 " --> pdb=" O UNK 1 511 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N UNK 1 516 " --> pdb=" O UNK 1 513 " (cutoff:3.500A) Processing helix chain '1' and resid 542 through 570 removed outlier: 3.810A pdb=" N CYS 1 550 " --> pdb=" O LEU 1 547 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS 1 557 " --> pdb=" O HIS 1 554 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS 1 563 " --> pdb=" O PHE 1 560 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE 1 564 " --> pdb=" O LEU 1 561 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER 1 570 " --> pdb=" O HIS 1 567 " (cutoff:3.500A) Processing helix chain '1' and resid 576 through 603 Processing helix chain '1' and resid 607 through 638 Proline residue: 1 618 - end of helix Processing helix chain '2' and resid 4 through 16 Processing helix chain '2' and resid 19 through 25 Processing helix chain '2' and resid 28 through 37 removed outlier: 3.996A pdb=" N CYS 2 32 " --> pdb=" O SER 2 28 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU 2 33 " --> pdb=" O PRO 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 50 Processing helix chain '2' and resid 59 through 66 Processing helix chain '2' and resid 71 through 83 Processing helix chain '2' and resid 102 through 112 Processing helix chain '2' and resid 117 through 122 Processing helix chain '2' and resid 132 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 194 Processing helix chain '2' and resid 197 through 210 removed outlier: 3.614A pdb=" N UNK 2 210 " --> pdb=" O UNK 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 224 Processing helix chain '2' and resid 226 through 228 No H-bonds generated for 'chain '2' and resid 226 through 228' Processing helix chain '2' and resid 237 through 240 No H-bonds generated for 'chain '2' and resid 237 through 240' Processing helix chain '2' and resid 244 through 256 removed outlier: 3.688A pdb=" N GLN 2 251 " --> pdb=" O ARG 2 247 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 280 Processing helix chain '2' and resid 381 through 388 Processing helix chain '2' and resid 394 through 403 Processing helix chain '2' and resid 408 through 418 Processing helix chain '2' and resid 435 through 449 Processing helix chain '2' and resid 465 through 477 Processing helix chain '2' and resid 498 through 507 Processing helix chain '3' and resid 20 through 22 No H-bonds generated for 'chain '3' and resid 20 through 22' Processing helix chain '3' and resid 40 through 49 removed outlier: 3.948A pdb=" N ARG 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 76 through 92 Processing helix chain '3' and resid 104 through 122 Processing helix chain '3' and resid 128 through 144 Processing helix chain '4' and resid 34 through 41 Processing helix chain '4' and resid 50 through 67 Processing helix chain '4' and resid 90 through 96 Processing helix chain '4' and resid 108 through 111 No H-bonds generated for 'chain '4' and resid 108 through 111' Processing helix chain '4' and resid 116 through 135 Processing helix chain '4' and resid 138 through 142 Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 190 through 206 removed outlier: 4.415A pdb=" N ILE 4 194 " --> pdb=" O ILE 4 190 " (cutoff:3.500A) Proline residue: 4 195 - end of helix Processing helix chain '4' and resid 222 through 230 Processing helix chain '4' and resid 244 through 255 removed outlier: 3.953A pdb=" N ILE 4 254 " --> pdb=" O THR 4 250 " (cutoff:3.500A) Processing helix chain '4' and resid 305 through 307 No H-bonds generated for 'chain '4' and resid 305 through 307' Processing helix chain '4' and resid 314 through 320 Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 44 through 62 removed outlier: 5.421A pdb=" N GLU 5 48 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU 5 53 " --> pdb=" O VAL 5 50 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS 5 60 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN 5 61 " --> pdb=" O LEU 5 58 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE 5 62 " --> pdb=" O SER 5 59 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 197 Processing helix chain '6' and resid 210 through 221 Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 281 removed outlier: 3.733A pdb=" N ASN 6 281 " --> pdb=" O CYS 6 277 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 305 Processing helix chain '6' and resid 373 through 383 Processing helix chain '6' and resid 394 through 397 No H-bonds generated for 'chain '6' and resid 394 through 397' Processing helix chain '6' and resid 418 through 421 No H-bonds generated for 'chain '6' and resid 418 through 421' Processing helix chain '6' and resid 438 through 446 Processing helix chain '6' and resid 452 through 455 Processing helix chain '7' and resid 364 through 375 removed outlier: 4.432A pdb=" N LYS 7 372 " --> pdb=" O LYS 7 368 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET 7 373 " --> pdb=" O SER 7 369 " (cutoff:3.500A) Processing helix chain '7' and resid 392 through 403 Processing helix chain '7' and resid 414 through 427 Processing helix chain '7' and resid 457 through 461 Processing helix chain '7' and resid 470 through 478 removed outlier: 3.638A pdb=" N UNK 7 476 " --> pdb=" O UNK 7 472 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 496 through 504 Processing helix chain '7' and resid 524 through 530 removed outlier: 3.713A pdb=" N LEU 7 530 " --> pdb=" O LEU 7 527 " (cutoff:3.500A) Processing helix chain '7' and resid 540 through 546 Processing helix chain '7' and resid 563 through 571 Processing helix chain '7' and resid 574 through 581 removed outlier: 3.606A pdb=" N ARG 7 577 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 601 Processing helix chain '7' and resid 612 through 622 Processing helix chain '7' and resid 633 through 645 Processing helix chain '7' and resid 656 through 660 Processing helix chain '7' and resid 680 through 693 Processing helix chain '7' and resid 716 through 728 removed outlier: 4.054A pdb=" N LYS 7 721 " --> pdb=" O TYR 7 717 " (cutoff:3.500A) Processing helix chain '7' and resid 742 through 744 No H-bonds generated for 'chain '7' and resid 742 through 744' Processing helix chain '7' and resid 753 through 769 Processing helix chain 'Z' and resid 19 through 28 removed outlier: 3.731A pdb=" N UNK Z 27 " --> pdb=" O UNK Z 23 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.595A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 250 through 252 Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 5.907A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.866A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.687A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 848 through 850 removed outlier: 3.624A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 878 through 882 Processing sheet with id= J, first strand: chain 'A' and resid 1115 through 1118 removed outlier: 3.527A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.874A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1290 through 1292 Processing sheet with id= M, first strand: chain 'B' and resid 69 through 73 Processing sheet with id= N, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.666A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= P, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= Q, first strand: chain 'B' and resid 215 through 218 Processing sheet with id= R, first strand: chain 'B' and resid 224 through 227 removed outlier: 7.072A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 497 through 499 Processing sheet with id= T, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= U, first strand: chain 'B' and resid 614 through 618 Processing sheet with id= V, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.798A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 1010 through 1012 removed outlier: 4.058A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= Y, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= Z, first strand: chain 'B' and resid 578 through 582 removed outlier: 4.106A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 839 through 842 removed outlier: 7.671A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 177 through 180 removed outlier: 6.422A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 97 through 104 removed outlier: 3.570A pdb=" N SER C 48 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.730A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AF, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.445A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AH, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AI, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.281A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 106 through 109 removed outlier: 4.061A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER G 152 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= AL, first strand: chain 'H' and resid 7 through 11 removed outlier: 7.221A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 15 through 19 Processing sheet with id= AN, first strand: chain 'I' and resid 83 through 86 Processing sheet with id= AO, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.584A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 34 through 37 Processing sheet with id= AQ, first strand: chain 'O' and resid 102 through 106 removed outlier: 3.842A pdb=" N ILE O 106 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL O 161 " --> pdb=" O GLN O 68 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE O 70 " --> pdb=" O ASN O 159 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN O 159 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU O 186 " --> pdb=" O PHE O 190 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLY O 192 " --> pdb=" O SER O 184 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER O 184 " --> pdb=" O GLY O 192 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 103 through 105 removed outlier: 6.764A pdb=" N PHE Q 384 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 119 through 121 removed outlier: 6.831A pdb=" N TYR Q 393 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 138 through 141 Processing sheet with id= AU, first strand: chain 'R' and resid 94 through 98 Processing sheet with id= AV, first strand: chain 'R' and resid 338 through 340 Processing sheet with id= AW, first strand: chain 'R' and resid 64 through 68 removed outlier: 5.971A pdb=" N ARG R 66 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS R 211 " --> pdb=" O GLN R 138 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL R 134 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'R' and resid 121 through 126 removed outlier: 6.612A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'U' and resid 243 through 245 Processing sheet with id= AZ, first strand: chain 'U' and resid 278 through 284 removed outlier: 3.864A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'V' and resid 60 through 63 Processing sheet with id= BB, first strand: chain 'V' and resid 110 through 116 removed outlier: 6.253A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'W' and resid 67 through 72 Processing sheet with id= BD, first strand: chain 'X' and resid 169 through 172 removed outlier: 4.319A pdb=" N THR X 177 " --> pdb=" O ASP X 172 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '0' and resid 478 through 480 removed outlier: 3.661A pdb=" N VAL 0 478 " --> pdb=" O ASN 0 37 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL 0 456 " --> pdb=" O SER 0 38 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU 0 40 " --> pdb=" O VAL 0 456 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE 0 458 " --> pdb=" O LEU 0 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE 0 206 " --> pdb=" O TYR 0 71 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER 0 73 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR 0 208 " --> pdb=" O SER 0 73 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain '0' and resid 251 through 253 Processing sheet with id= BG, first strand: chain '0' and resid 678 through 681 removed outlier: 3.512A pdb=" N VAL 0 538 " --> pdb=" O THR 0 619 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET 0 537 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N HIS 0 566 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N LEU 0 599 " --> pdb=" O HIS 0 566 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU 0 568 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain '0' and resid 494 through 498 removed outlier: 6.241A pdb=" N ILE 0 697 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE 0 497 " --> pdb=" O ILE 0 697 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLN 0 699 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain '1' and resid 4 through 9 Processing sheet with id= BJ, first strand: chain '1' and resid 85 through 90 removed outlier: 4.056A pdb=" N LYS 1 47 " --> pdb=" O ILE 1 63 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain '2' and resid 87 through 91 Processing sheet with id= BL, first strand: chain '2' and resid 173 through 176 Processing sheet with id= BM, first strand: chain '2' and resid 456 through 459 removed outlier: 3.729A pdb=" N TRP 2 483 " --> pdb=" O PHE 2 492 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain '2' and resid 259 through 262 removed outlier: 6.238A pdb=" N ILE 2 268 " --> pdb=" O LYS 2 262 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain '3' and resid 28 through 30 Processing sheet with id= BP, first strand: chain '4' and resid 82 through 85 removed outlier: 5.911A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU 4 179 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain '5' and resid 8 through 11 Processing sheet with id= BR, first strand: chain '6' and resid 178 through 183 removed outlier: 6.244A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE 6 236 " --> pdb=" O LYS 6 262 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU 6 264 " --> pdb=" O PHE 6 236 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain '6' and resid 322 through 324 removed outlier: 5.295A pdb=" N MET 6 369 " --> pdb=" O UNK 6 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain '6' and resid 326 through 328 removed outlier: 3.549A pdb=" N THR 6 326 " --> pdb=" O PHE 6 348 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain '6' and resid 390 through 392 Processing sheet with id= BV, first strand: chain '7' and resid 451 through 456 removed outlier: 6.809A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA 7 509 " --> pdb=" O ILE 7 485 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N LEU 7 487 " --> pdb=" O ALA 7 509 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU 7 511 " --> pdb=" O LEU 7 487 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG 7 380 " --> pdb=" O LYS 7 510 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLY 7 512 " --> pdb=" O ARG 7 380 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N THR 7 514 " --> pdb=" O GLY 7 382 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE 7 384 " --> pdb=" O THR 7 514 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL 7 385 " --> pdb=" O LEU 7 535 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU 7 537 " --> pdb=" O VAL 7 385 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain '7' and resid 732 through 736 removed outlier: 3.789A pdb=" N ALA 7 732 " --> pdb=" O VAL 7 552 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU 7 556 " --> pdb=" O LYS 7 734 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'Z' and resid 3 through 5 removed outlier: 4.352A pdb=" N UNK Z 3 " --> pdb=" O UNK Z 15 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'Z' and resid 30 through 35 removed outlier: 6.871A pdb=" N UNK Z 40 " --> pdb=" O UNK Z 32 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N UNK Z 34 " --> pdb=" O UNK Z 38 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N UNK Z 38 " --> pdb=" O UNK Z 34 " (cutoff:3.500A) 2527 hydrogen bonds defined for protein. 7029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 164 hydrogen bonds 328 hydrogen bond angles 0 basepair planarities 69 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 31.08 Time building geometry restraints manager: 21.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.54: 63231 1.54 - 1.87: 922 1.87 - 2.20: 0 2.20 - 2.53: 12 2.53 - 2.86: 1 Bond restraints: 64166 Sorted by residual: bond pdb=" C LEU X 181 " pdb=" N THR X 183 " ideal model delta sigma weight residual 1.332 2.865 -1.532 1.40e-02 5.10e+03 1.20e+04 bond pdb=" C UNK 0 321 " pdb=" N UNK 0 322 " ideal model delta sigma weight residual 1.329 1.401 -0.072 1.40e-02 5.10e+03 2.62e+01 bond pdb=" C THR 0 533 " pdb=" N PRO 0 534 " ideal model delta sigma weight residual 1.334 1.432 -0.098 2.34e-02 1.83e+03 1.76e+01 bond pdb=" C THR B1213 " pdb=" N PRO B1214 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.43e+01 bond pdb=" CA MET 1 88 " pdb=" C MET 1 88 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.03e-02 9.43e+03 1.28e+01 ... (remaining 64161 not shown) Histogram of bond angle deviations from ideal: 70.85 - 83.49: 12 83.49 - 96.13: 0 96.13 - 108.76: 4158 108.76 - 121.40: 67107 121.40 - 134.04: 16223 Bond angle restraints: 87500 Sorted by residual: angle pdb=" O LEU X 181 " pdb=" C LEU X 181 " pdb=" N THR X 183 " ideal model delta sigma weight residual 122.59 99.59 23.00 1.33e+00 5.65e-01 2.99e+02 angle pdb=" C ILE E 127 " pdb=" N PRO E 128 " pdb=" CA PRO E 128 " ideal model delta sigma weight residual 119.66 124.41 -4.75 7.20e-01 1.93e+00 4.36e+01 angle pdb=" C VAL A1146 " pdb=" N THR A1147 " pdb=" CA THR A1147 " ideal model delta sigma weight residual 122.77 114.37 8.40 1.33e+00 5.65e-01 3.99e+01 angle pdb=" C ILE 4 288 " pdb=" N CYS 4 289 " pdb=" CA CYS 4 289 " ideal model delta sigma weight residual 120.63 113.51 7.12 1.36e+00 5.41e-01 2.74e+01 angle pdb=" N CYS I 29 " pdb=" CA CYS I 29 " pdb=" C CYS I 29 " ideal model delta sigma weight residual 108.34 100.59 7.75 1.64e+00 3.72e-01 2.24e+01 ... (remaining 87495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.92: 37760 31.92 - 63.84: 967 63.84 - 95.75: 69 95.75 - 127.67: 0 127.67 - 159.59: 2 Dihedral angle restraints: 38798 sinusoidal: 14890 harmonic: 23908 Sorted by residual: dihedral pdb=" CA LEU X 181 " pdb=" C LEU X 181 " pdb=" N THR X 183 " pdb=" CA THR X 183 " ideal model delta harmonic sigma weight residual -180.00 -96.03 -83.97 0 5.00e+00 4.00e-02 2.82e+02 dihedral pdb=" CA LEU 2 39 " pdb=" C LEU 2 39 " pdb=" N PRO 2 40 " pdb=" CA PRO 2 40 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA UNK 1 350 " pdb=" C UNK 1 350 " pdb=" N UNK 1 351 " pdb=" CA UNK 1 351 " ideal model delta harmonic sigma weight residual 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 38795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 8466 0.050 - 0.101: 1385 0.101 - 0.151: 338 0.151 - 0.202: 11 0.202 - 0.252: 5 Chirality restraints: 10205 Sorted by residual: chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C4' DG N 45 " pdb=" C5' DG N 45 " pdb=" O4' DG N 45 " pdb=" C3' DG N 45 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA CYS I 29 " pdb=" N CYS I 29 " pdb=" C CYS I 29 " pdb=" CB CYS I 29 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 10202 not shown) Planarity restraints: 10902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU X 181 " 0.126 2.00e-02 2.50e+03 1.84e-01 3.39e+02 pdb=" C LEU X 181 " -0.313 2.00e-02 2.50e+03 pdb=" O LEU X 181 " 0.141 2.00e-02 2.50e+03 pdb=" N THR X 183 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 43 " 0.046 2.00e-02 2.50e+03 2.92e-02 2.13e+01 pdb=" N1 DT N 43 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DT N 43 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT N 43 " -0.048 2.00e-02 2.50e+03 pdb=" N3 DT N 43 " 0.051 2.00e-02 2.50e+03 pdb=" C4 DT N 43 " 0.000 2.00e-02 2.50e+03 pdb=" O4 DT N 43 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DT N 43 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT N 43 " -0.020 2.00e-02 2.50e+03 pdb=" C6 DT N 43 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 44 " 0.033 2.00e-02 2.50e+03 2.03e-02 9.28e+00 pdb=" N1 DC N 44 " -0.050 2.00e-02 2.50e+03 pdb=" C2 DC N 44 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC N 44 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC N 44 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC N 44 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC N 44 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DC N 44 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC N 44 " 0.004 2.00e-02 2.50e+03 ... (remaining 10899 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 2 2.05 - 2.76: 9473 2.76 - 3.47: 85449 3.47 - 4.19: 146267 4.19 - 4.90: 250784 Nonbonded interactions: 491975 Sorted by model distance: nonbonded pdb=" N UNK 2 380 " pdb=" C UNK Z 43 " model vdw 1.336 3.350 nonbonded pdb=" O GLU I 54 " pdb=" N GLN I 89 " model vdw 1.928 2.520 nonbonded pdb=" NH1 ARG 0 594 " pdb=" O THR 6 241 " model vdw 2.080 2.520 nonbonded pdb=" NH1 ARG C 11 " pdb=" OH TYR C 209 " model vdw 2.121 2.520 nonbonded pdb=" O ARG J 48 " pdb=" OG1 THR J 52 " model vdw 2.145 2.440 ... (remaining 491970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 10.930 Check model and map are aligned: 0.700 Set scattering table: 0.450 Process input model: 168.200 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 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 : 0.007 1.532 64166 Z= 0.502 Angle : 0.541 23.000 87500 Z= 0.317 Chirality : 0.040 0.252 10205 Planarity : 0.004 0.184 10902 Dihedral : 12.581 159.590 23206 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 1.23 % Allowed : 6.46 % Favored : 92.31 % Rotamer: Outliers : 0.30 % Allowed : 4.17 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.08), residues: 7503 helix: -2.15 (0.07), residues: 3174 sheet: -1.75 (0.13), residues: 1259 loop : -2.44 (0.09), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 81 HIS 0.014 0.001 HIS A 80 PHE 0.023 0.001 PHE 0 437 TYR 0.012 0.001 TYR Q 401 ARG 0.006 0.000 ARG A1055 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15006 Ramachandran restraints generated. 7503 Oldfield, 0 Emsley, 7503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15006 Ramachandran restraints generated. 7503 Oldfield, 0 Emsley, 7503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2085 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 2068 time to evaluate : 5.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 2079 average time/residue: 0.6351 time to fit residues: 2177.5324 Evaluate side-chains 1051 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1046 time to evaluate : 5.442 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.4408 time to fit residues: 11.3980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 597 optimal weight: 6.9990 chunk 535 optimal weight: 0.7980 chunk 297 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 361 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 chunk 554 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 336 optimal weight: 7.9990 chunk 412 optimal weight: 0.0970 chunk 642 optimal weight: 9.9990 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 64 ASN A 311 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 640 GLN A 654 ASN A 698 GLN A 745 GLN A 760 GLN A 768 GLN A 802 ASN A 953 ASN A 965 GLN A 968 GLN A1130 GLN A1218 GLN A1270 ASN ** A1387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 395 GLN B 415 GLN B 433 GLN B 440 HIS B 494 HIS B 573 GLN B 657 HIS B 667 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B 958 GLN B1062 HIS ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1193 GLN B1195 HIS C 73 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 HIS C 224 GLN C 231 ASN C 242 GLN C 252 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN G 10 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN K 52 ASN K 112 GLN M 90 ASN M 124 ASN M 285 ASN M 300 GLN O 91 ASN O 158 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN R 223 GLN ** U 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 55 ASN W 50 ASN ** W 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 178 GLN X 199 GLN X 223 GLN X 279 GLN ** 0 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 265 ASN 0 521 ASN ** 0 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 3 HIS 1 75 ASN ** 1 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 92 ASN 1 258 ASN 5 11 GLN 6 146 HIS 6 212 ASN 6 248 HIS ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN 7 491 HIS 7 508 HIS ** 7 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 592 GLN 7 648 GLN ** 7 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 676 HIS ** 7 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 738 HIS 7 740 HIS 7 767 ASN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 64166 Z= 0.404 Angle : 0.801 12.401 87500 Z= 0.419 Chirality : 0.045 0.222 10205 Planarity : 0.006 0.075 10902 Dihedral : 14.212 161.736 10332 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.56 % Favored : 95.10 % Rotamer: Outliers : 0.46 % Allowed : 4.25 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 7505 helix: -0.11 (0.09), residues: 3178 sheet: -1.17 (0.14), residues: 1162 loop : -1.76 (0.10), residues: 3165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP 1 210 HIS 0.024 0.002 HIS 1 3 PHE 0.039 0.003 PHE 7 701 TYR 0.035 0.002 TYR H 129 ARG 0.014 0.001 ARG X 276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1156 time to evaluate : 5.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 1179 average time/residue: 0.5984 time to fit residues: 1187.9253 Evaluate side-chains 805 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 795 time to evaluate : 5.445 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4512 time to fit residues: 15.6072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 356 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 534 optimal weight: 2.9990 chunk 437 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 643 optimal weight: 0.2980 chunk 694 optimal weight: 9.9990 chunk 572 optimal weight: 1.9990 chunk 637 optimal weight: 0.8980 chunk 219 optimal weight: 10.0000 chunk 515 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 313 GLN A 525 GLN A1218 GLN B 53 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 HIS ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN C 102 GLN C 206 ASN D 143 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 319 HIS U 33 GLN 0 362 HIS 0 651 ASN 0 707 ASN ** 0 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 182 GLN 2 469 ASN ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 211 GLN 7 567 GLN ** 7 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 64166 Z= 0.213 Angle : 0.586 11.819 87500 Z= 0.307 Chirality : 0.042 0.295 10205 Planarity : 0.004 0.050 10902 Dihedral : 14.126 161.700 10332 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.94 % Favored : 94.79 % Rotamer: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.10), residues: 7505 helix: 0.58 (0.09), residues: 3182 sheet: -0.96 (0.14), residues: 1233 loop : -1.59 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 1 210 HIS 0.014 0.001 HIS B 300 PHE 0.037 0.002 PHE 1 91 TYR 0.020 0.001 TYR 7 731 ARG 0.009 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1075 time to evaluate : 5.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 1082 average time/residue: 0.6217 time to fit residues: 1143.3233 Evaluate side-chains 778 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 775 time to evaluate : 5.455 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4757 time to fit residues: 9.7660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 635 optimal weight: 0.8980 chunk 483 optimal weight: 9.9990 chunk 333 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 431 optimal weight: 0.0000 chunk 645 optimal weight: 3.9990 chunk 683 optimal weight: 9.9990 chunk 337 optimal weight: 4.9990 chunk 611 optimal weight: 9.9990 chunk 184 optimal weight: 0.4980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 339 ASN A 451 HIS A1218 GLN B 53 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN G 10 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN L 53 HIS M 234 GLN M 285 ASN O 68 GLN R 131 ASN R 223 GLN U 36 GLN ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 242 ASN ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 491 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 64166 Z= 0.186 Angle : 0.562 12.196 87500 Z= 0.294 Chirality : 0.041 0.234 10205 Planarity : 0.004 0.063 10902 Dihedral : 14.104 162.073 10332 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.62 % Favored : 95.12 % Rotamer: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.10), residues: 7505 helix: 0.90 (0.09), residues: 3170 sheet: -0.65 (0.15), residues: 1143 loop : -1.50 (0.11), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP 1 210 HIS 0.011 0.001 HIS B 300 PHE 0.036 0.002 PHE 1 91 TYR 0.023 0.001 TYR Q 98 ARG 0.011 0.000 ARG 0 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1041 time to evaluate : 5.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 1046 average time/residue: 0.5898 time to fit residues: 1052.3602 Evaluate side-chains 751 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 749 time to evaluate : 5.493 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5053 time to fit residues: 8.9930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 569 optimal weight: 0.8980 chunk 387 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 508 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 583 optimal weight: 7.9990 chunk 472 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 613 optimal weight: 40.0000 chunk 172 optimal weight: 0.9980 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 736 ASN A 996 ASN A1140 HIS A1211 GLN A1218 GLN ** A1387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 842 ASN B 932 HIS ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN E 101 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 90 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 HIS ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 HIS W 178 GLN 0 88 ASN 0 117 HIS ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 362 HIS ** 0 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 476 GLN ** 6 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 64166 Z= 0.427 Angle : 0.750 12.273 87500 Z= 0.394 Chirality : 0.044 0.255 10205 Planarity : 0.005 0.094 10902 Dihedral : 14.335 160.577 10332 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.60 % Rotamer: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.10), residues: 7505 helix: 0.70 (0.09), residues: 3148 sheet: -0.91 (0.15), residues: 1195 loop : -1.57 (0.11), residues: 3162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP 1 210 HIS 0.014 0.002 HIS J 53 PHE 0.047 0.003 PHE I 100 TYR 0.033 0.002 TYR J 44 ARG 0.013 0.001 ARG 0 520 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 926 time to evaluate : 5.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 928 average time/residue: 0.5996 time to fit residues: 945.8425 Evaluate side-chains 671 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 670 time to evaluate : 5.471 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5138 time to fit residues: 8.1560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 229 optimal weight: 0.9990 chunk 615 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 401 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 684 optimal weight: 5.9990 chunk 567 optimal weight: 20.0000 chunk 316 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 359 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A1008 GLN A1211 GLN A1218 GLN ** A1387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 52 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 ASN 0 88 ASN ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 682 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 64166 Z= 0.209 Angle : 0.588 11.834 87500 Z= 0.308 Chirality : 0.042 0.225 10205 Planarity : 0.004 0.064 10902 Dihedral : 14.259 160.215 10332 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.02 % Allowed : 1.72 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 7505 helix: 1.05 (0.10), residues: 3147 sheet: -0.71 (0.15), residues: 1163 loop : -1.46 (0.11), residues: 3195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP 1 210 HIS 0.015 0.001 HIS 7 598 PHE 0.034 0.002 PHE D 175 TYR 0.024 0.001 TYR B1092 ARG 0.008 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 945 time to evaluate : 5.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 946 average time/residue: 0.6152 time to fit residues: 991.7301 Evaluate side-chains 693 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 693 time to evaluate : 5.497 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 659 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 389 optimal weight: 6.9990 chunk 499 optimal weight: 40.0000 chunk 387 optimal weight: 0.0030 chunk 575 optimal weight: 8.9990 chunk 381 optimal weight: 1.9990 chunk 681 optimal weight: 9.9990 chunk 426 optimal weight: 0.9980 chunk 415 optimal weight: 10.0000 chunk 314 optimal weight: 0.9980 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 802 ASN A1211 GLN A1218 GLN ** A1387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 HIS ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 258 ASN 2 476 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 64166 Z= 0.213 Angle : 0.595 19.591 87500 Z= 0.310 Chirality : 0.042 0.273 10205 Planarity : 0.004 0.082 10902 Dihedral : 14.198 159.914 10332 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.62 % Favored : 94.14 % Rotamer: Outliers : 0.02 % Allowed : 1.32 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.10), residues: 7505 helix: 1.18 (0.10), residues: 3137 sheet: -0.66 (0.15), residues: 1171 loop : -1.40 (0.11), residues: 3197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP 1 210 HIS 0.020 0.001 HIS M 158 PHE 0.028 0.002 PHE A1410 TYR 0.016 0.001 TYR 7 731 ARG 0.011 0.000 ARG 0 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 926 time to evaluate : 5.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 927 average time/residue: 0.5979 time to fit residues: 945.1592 Evaluate side-chains 689 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 689 time to evaluate : 5.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 421 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 406 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 433 optimal weight: 4.9990 chunk 464 optimal weight: 10.0000 chunk 336 optimal weight: 0.0010 chunk 63 optimal weight: 4.9990 chunk 535 optimal weight: 9.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1211 GLN A1218 GLN ** A1387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 54 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 476 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 64166 Z= 0.309 Angle : 0.648 10.403 87500 Z= 0.341 Chirality : 0.042 0.260 10205 Planarity : 0.004 0.070 10902 Dihedral : 14.272 159.067 10332 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.14 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.10), residues: 7505 helix: 1.09 (0.09), residues: 3134 sheet: -0.75 (0.15), residues: 1152 loop : -1.45 (0.11), residues: 3219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 1 210 HIS 0.014 0.001 HIS M 158 PHE 0.027 0.002 PHE A 22 TYR 0.020 0.002 TYR B 797 ARG 0.015 0.001 ARG 6 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 897 time to evaluate : 5.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 897 average time/residue: 0.6018 time to fit residues: 926.3699 Evaluate side-chains 652 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 5.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 619 optimal weight: 20.0000 chunk 652 optimal weight: 20.0000 chunk 595 optimal weight: 3.9990 chunk 635 optimal weight: 2.9990 chunk 382 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 498 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 573 optimal weight: 0.8980 chunk 600 optimal weight: 10.0000 chunk 632 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1211 GLN A1218 GLN ** A1387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 3 HIS ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.7216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 64166 Z= 0.259 Angle : 0.623 10.259 87500 Z= 0.327 Chirality : 0.042 0.298 10205 Planarity : 0.004 0.062 10902 Dihedral : 14.264 158.347 10332 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.96 % Favored : 93.82 % Rotamer: Outliers : 0.02 % Allowed : 0.53 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.10), residues: 7505 helix: 1.20 (0.10), residues: 3122 sheet: -0.81 (0.15), residues: 1181 loop : -1.40 (0.11), residues: 3202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP 1 210 HIS 0.008 0.001 HIS M 158 PHE 0.031 0.002 PHE 6 301 TYR 0.016 0.001 TYR B 797 ARG 0.012 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 893 time to evaluate : 5.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 894 average time/residue: 0.6058 time to fit residues: 927.9578 Evaluate side-chains 648 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 648 time to evaluate : 5.594 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 416 optimal weight: 10.0000 chunk 671 optimal weight: 50.0000 chunk 409 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 466 optimal weight: 3.9990 chunk 704 optimal weight: 30.0000 chunk 648 optimal weight: 10.0000 chunk 560 optimal weight: 7.9990 chunk 58 optimal weight: 0.3980 chunk 433 optimal weight: 8.9990 chunk 343 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS A1211 GLN A1218 GLN ** A1387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 362 HIS ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 589 GLN 7 641 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.7601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 64166 Z= 0.349 Angle : 0.689 9.691 87500 Z= 0.363 Chirality : 0.043 0.300 10205 Planarity : 0.004 0.063 10902 Dihedral : 14.365 156.761 10332 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.00 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.10), residues: 7505 helix: 1.01 (0.09), residues: 3107 sheet: -0.93 (0.15), residues: 1185 loop : -1.49 (0.11), residues: 3213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP 1 210 HIS 0.010 0.001 HIS A 399 PHE 0.029 0.002 PHE D 175 TYR 0.025 0.002 TYR B 666 ARG 0.013 0.001 ARG A 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15010 Ramachandran restraints generated. 7505 Oldfield, 0 Emsley, 7505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 841 time to evaluate : 5.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 841 average time/residue: 0.6072 time to fit residues: 873.2257 Evaluate side-chains 613 residues out of total 6830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 613 time to evaluate : 5.608 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 445 optimal weight: 7.9990 chunk 597 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 517 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 561 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 576 optimal weight: 4.9990 chunk 71 optimal weight: 0.0170 chunk 103 optimal weight: 0.6980 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN A1218 GLN ** A1387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 GLN ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 GLN O 158 GLN ** Q 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 362 HIS ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.068456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.046051 restraints weight = 362617.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.047765 restraints weight = 234957.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.048138 restraints weight = 159030.847| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 64166 Z= 0.180 Angle : 0.601 9.823 87500 Z= 0.313 Chirality : 0.042 0.273 10205 Planarity : 0.004 0.065 10902 Dihedral : 14.257 156.533 10332 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.28 % Favored : 94.51 % Rotamer: Outliers : 0.02 % Allowed : 0.30 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.10), residues: 7505 helix: 1.33 (0.10), residues: 3105 sheet: -0.71 (0.15), residues: 1136 loop : -1.37 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP 1 210 HIS 0.008 0.001 HIS M 158 PHE 0.027 0.001 PHE W 15 TYR 0.026 0.001 TYR B 890 ARG 0.008 0.000 ARG 1 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16008.48 seconds wall clock time: 281 minutes 2.98 seconds (16862.98 seconds total)