Starting phenix.real_space_refine on Fri Aug 9 16:51:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q91_18267/08_2024/8q91_18267.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q91_18267/08_2024/8q91_18267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q91_18267/08_2024/8q91_18267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q91_18267/08_2024/8q91_18267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q91_18267/08_2024/8q91_18267.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q91_18267/08_2024/8q91_18267.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 106 5.49 5 S 93 5.16 5 C 16557 2.51 5 N 4707 2.21 5 O 5243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 169": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 946": "OE1" <-> "OE2" Residue "A GLU 1171": "OE1" <-> "OE2" Residue "A TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1219": "OE1" <-> "OE2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "A ASP 1441": "OD1" <-> "OD2" Residue "A PHE 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 668": "OE1" <-> "OE2" Residue "C GLU 716": "OE1" <-> "OE2" Residue "C GLU 945": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26706 Number of models: 1 Model: "" Number of chains: 15 Chain: "F" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 887 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 13247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1627, 13247 Classifications: {'peptide': 1627} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 3, 'PTRANS': 90, 'TRANS': 1533} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 384 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Chain: "5" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2192 Classifications: {'RNA': 104} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 38, 'rna3p_pyr': 43} Link IDs: {'rna2p': 22, 'rna3p': 81} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 300 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 147 Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain breaks: 1 Chain: "C" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6629 Classifications: {'peptide': 847} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 49, 'TRANS': 797} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "m" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 356 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "n" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 364 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "i" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 401 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "j" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 487 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 165 Chain: "k" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 414 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "h" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 360 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 125 Chain: "l" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 381 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.64, per 1000 atoms: 0.62 Number of scatterers: 26706 At special positions: 0 Unit cell: (123.298, 165.094, 219.429, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 106 15.00 O 5243 8.00 N 4707 7.00 C 16557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.06 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: 11.60 Conformation dependent library (CDL) restraints added in 4.5 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6276 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 20 sheets defined 43.7% alpha, 17.0% beta 34 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 10.96 Creating SS restraints... Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.895A pdb=" N VAL F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 72 " --> pdb=" O SER F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 92 through 99 Processing helix chain 'F' and resid 117 through 122 removed outlier: 3.577A pdb=" N ASN F 122 " --> pdb=" O SER F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'F' and resid 196 through 212 Processing helix chain 'F' and resid 216 through 220 Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'A' and resid 62 through 72 removed outlier: 4.345A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.802A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.737A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 156 removed outlier: 3.623A pdb=" N ARG A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 398 through 404 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 489 through 510 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.567A pdb=" N LYS A 537 " --> pdb=" O LYS A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 566 removed outlier: 3.780A pdb=" N HIS A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 590 through 596 removed outlier: 3.671A pdb=" N ARG A 593 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR A 596 " --> pdb=" O ARG A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.137A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 656 removed outlier: 3.832A pdb=" N MET A 641 " --> pdb=" O TRP A 637 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 681 through 696 Processing helix chain 'A' and resid 704 through 722 Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 798 Processing helix chain 'A' and resid 802 through 820 Processing helix chain 'A' and resid 834 through 850 removed outlier: 3.894A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 888 Processing helix chain 'A' and resid 912 through 934 Processing helix chain 'A' and resid 947 through 961 Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.979A pdb=" N LEU A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1013 Processing helix chain 'A' and resid 1036 through 1054 Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1102 through 1117 Processing helix chain 'A' and resid 1135 through 1139 Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.505A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1173 Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1274 Processing helix chain 'A' and resid 1274 through 1281 removed outlier: 4.034A pdb=" N VAL A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1336 through 1341 removed outlier: 3.508A pdb=" N LEU A1340 " --> pdb=" O GLN A1337 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A1341 " --> pdb=" O SER A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1372 removed outlier: 3.583A pdb=" N ARG A1370 " --> pdb=" O ASN A1367 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1372 " --> pdb=" O TYR A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1400 Processing helix chain 'A' and resid 1408 through 1412 removed outlier: 3.520A pdb=" N TRP A1412 " --> pdb=" O GLU A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1424 removed outlier: 3.704A pdb=" N GLN A1424 " --> pdb=" O THR A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1435 through 1444 removed outlier: 4.022A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1467 through 1479 Processing helix chain 'A' and resid 1479 through 1487 removed outlier: 4.037A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1493 Processing helix chain 'A' and resid 1531 through 1538 Processing helix chain 'A' and resid 1539 through 1542 Processing helix chain 'A' and resid 1566 through 1577 Processing helix chain 'A' and resid 1580 through 1600 Processing helix chain 'A' and resid 1601 through 1605 Processing helix chain 'A' and resid 1617 through 1621 Processing helix chain 'A' and resid 1675 through 1689 removed outlier: 3.910A pdb=" N THR A1689 " --> pdb=" O LEU A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1737 Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'E' and resid 96 through 114 Processing helix chain 'E' and resid 116 through 127 Processing helix chain 'E' and resid 138 through 150 removed outlier: 5.207A pdb=" N ASP E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 145 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 157 removed outlier: 3.622A pdb=" N GLU E 156 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 141 through 151 removed outlier: 3.854A pdb=" N PHE C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.752A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 260 through 265 removed outlier: 3.831A pdb=" N ILE C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 312 through 315 Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.622A pdb=" N LYS C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 387 Processing helix chain 'C' and resid 391 through 400 removed outlier: 3.766A pdb=" N THR C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 437 removed outlier: 3.577A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 5.013A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 459 through 468 removed outlier: 3.686A pdb=" N CYS C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 695 through 702 removed outlier: 3.671A pdb=" N ASP C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 723 removed outlier: 3.517A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 755 through 777 removed outlier: 3.699A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN C 768 " --> pdb=" O ASP C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 823 removed outlier: 3.986A pdb=" N THR C 811 " --> pdb=" O GLN C 807 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 852 removed outlier: 3.725A pdb=" N ARG C 852 " --> pdb=" O THR C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 881 removed outlier: 4.119A pdb=" N PHE C 881 " --> pdb=" O ILE C 878 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 878 through 881' Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 942 removed outlier: 3.698A pdb=" N GLU C 932 " --> pdb=" O HIS C 928 " (cutoff:3.500A) Processing helix chain 'm' and resid 6 through 14 removed outlier: 3.517A pdb=" N LEU m 14 " --> pdb=" O PHE m 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 13 Processing helix chain 'n' and resid 64 through 67 Processing helix chain 'i' and resid 3 through 9 Processing helix chain 'i' and resid 75 through 80 Processing helix chain 'j' and resid 18 through 23 Processing helix chain 'j' and resid 29 through 39 removed outlier: 3.551A pdb=" N THR j 33 " --> pdb=" O LEU j 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER j 35 " --> pdb=" O VAL j 31 " (cutoff:3.500A) Processing helix chain 'k' and resid 4 through 13 Processing helix chain 'k' and resid 74 through 84 Proline residue: k 81 - end of helix Processing helix chain 'h' and resid 7 through 11 Processing helix chain 'l' and resid 16 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA3, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA5, first strand: chain 'A' and resid 904 through 910 removed outlier: 3.722A pdb=" N LEU A 901 " --> pdb=" O HIS A 904 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 894 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 5.341A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A1095 " --> pdb=" O SER A 979 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1185 through 1189 removed outlier: 3.581A pdb=" N ALA A1226 " --> pdb=" O LEU A1216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1342 through 1346 Processing sheet with id=AA9, first strand: chain 'A' and resid 1553 through 1554 removed outlier: 3.863A pdb=" N VAL A1553 " --> pdb=" O MET A1562 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1608 through 1611 removed outlier: 8.618A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N TYR A1635 " --> pdb=" O THR A1656 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N THR A1656 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N TRP A1637 " --> pdb=" O SER A1654 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N SER A1654 " --> pdb=" O TRP A1637 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL A1639 " --> pdb=" O MET A1652 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N MET A1652 " --> pdb=" O VAL A1639 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 184 through 191 removed outlier: 9.012A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ASP C 230 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AB4, first strand: chain 'C' and resid 523 through 526 removed outlier: 7.227A pdb=" N CYS C 476 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 497 " --> pdb=" O CYS C 476 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR C 478 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ARG C 495 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AB6, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.777A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.777A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 783 through 784 removed outlier: 6.402A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 783 through 784 removed outlier: 7.162A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.147A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASP C 793 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 745 " --> pdb=" O TRP C 733 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 18 through 23 removed outlier: 4.829A pdb=" N MET m 27 " --> pdb=" O LEU m 23 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU m 28 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU m 49 " --> pdb=" O GLU m 28 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS m 30 " --> pdb=" O THR m 47 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR m 47 " --> pdb=" O LYS m 30 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR m 32 " --> pdb=" O ALA m 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA m 45 " --> pdb=" O TYR m 32 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN m 43 " --> pdb=" O VAL m 34 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLN m 43 " --> pdb=" O VAL m 62 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL m 62 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA m 45 " --> pdb=" O GLY m 60 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY m 60 " --> pdb=" O ALA m 45 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N THR m 47 " --> pdb=" O HIS m 58 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS m 58 " --> pdb=" O THR m 47 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLU m 49 " --> pdb=" O SER m 56 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU m 61 " --> pdb=" O ARG j 111 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG j 111 " --> pdb=" O GLU m 61 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS j 51 " --> pdb=" O GLU j 72 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU j 72 " --> pdb=" O LYS j 51 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU j 53 " --> pdb=" O VAL j 70 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL j 70 " --> pdb=" O LEU j 53 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG j 55 " --> pdb=" O GLU j 68 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL j 66 " --> pdb=" O LYS j 57 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU j 67 " --> pdb=" O MET j 99 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER j 97 " --> pdb=" O ASN j 69 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS j 71 " --> pdb=" O TYR j 95 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR j 95 " --> pdb=" O LYS j 71 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET j 73 " --> pdb=" O ASP j 93 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP j 93 " --> pdb=" O MET j 73 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR j 75 " --> pdb=" O ASN j 91 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASN j 91 " --> pdb=" O THR j 75 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS j 98 " --> pdb=" O LEU i 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR i 16 " --> pdb=" O ILE i 69 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU i 13 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR i 28 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA i 42 " --> pdb=" O THR i 28 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR i 30 " --> pdb=" O LEU i 40 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU i 40 " --> pdb=" O THR i 30 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL i 32 " --> pdb=" O THR i 38 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR i 38 " --> pdb=" O VAL i 32 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU i 56 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS i 44 " --> pdb=" O GLN i 54 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLN i 54 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 14.070A pdb=" N LEU i 55 " --> pdb=" O GLY h 84 " (cutoff:3.500A) removed outlier: 12.299A pdb=" N GLY h 84 " --> pdb=" O LEU i 55 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR i 57 " --> pdb=" O VAL h 82 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL h 82 " --> pdb=" O THR i 57 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG h 16 " --> pdb=" O GLU h 83 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR h 30 " --> pdb=" O ASP h 44 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP h 44 " --> pdb=" O THR h 30 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS h 32 " --> pdb=" O LEU h 42 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU h 42 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE h 34 " --> pdb=" O LEU h 40 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU h 40 " --> pdb=" O PHE h 34 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLY h 68 " --> pdb=" O ASP h 44 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP h 46 " --> pdb=" O VAL h 66 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL h 66 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N PHE h 48 " --> pdb=" O LYS h 64 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LYS h 64 " --> pdb=" O PHE h 48 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU h 69 " --> pdb=" O LEU k 73 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLU k 21 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU k 71 " --> pdb=" O THR k 19 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR k 19 " --> pdb=" O LEU k 71 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU k 73 " --> pdb=" O ILE k 17 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE k 17 " --> pdb=" O LEU k 73 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL k 27 " --> pdb=" O VAL k 48 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL k 48 " --> pdb=" O VAL k 27 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG k 29 " --> pdb=" O ILE k 46 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE k 46 " --> pdb=" O ARG k 29 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN k 42 " --> pdb=" O ILE k 33 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN k 42 " --> pdb=" O TYR k 62 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR k 62 " --> pdb=" O GLN k 42 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER k 44 " --> pdb=" O GLN k 60 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN k 60 " --> pdb=" O SER k 44 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLN k 60 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA n 72 " --> pdb=" O GLN k 60 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET n 69 " --> pdb=" O LYS n 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS n 20 " --> pdb=" O MET n 69 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN n 28 " --> pdb=" O CYS n 45 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS n 45 " --> pdb=" O GLN n 28 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU l 86 " --> pdb=" O TRP l 34 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS l 46 " --> pdb=" O ASP l 60 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP l 60 " --> pdb=" O CYS l 46 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE l 48 " --> pdb=" O LEU l 58 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU l 58 " --> pdb=" O ILE l 48 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL l 57 " --> pdb=" O MET l 78 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET l 78 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP l 59 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS m 22 " --> pdb=" O LEU m 70 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE m 72 " --> pdb=" O MET m 20 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET m 20 " --> pdb=" O ILE m 72 " (cutoff:3.500A) 1201 hydrogen bonds defined for protein. 3360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 16.08 Time building geometry restraints manager: 12.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8493 1.34 - 1.46: 6507 1.46 - 1.58: 12116 1.58 - 1.70: 209 1.70 - 1.83: 152 Bond restraints: 27477 Sorted by residual: bond pdb=" N CYS C 144 " pdb=" CA CYS C 144 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.20e-02 6.94e+03 8.72e+00 bond pdb=" N LEU C 149 " pdb=" CA LEU C 149 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.35e-02 5.49e+03 8.65e+00 bond pdb=" N ASN m 41 " pdb=" CA ASN m 41 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.61e+00 bond pdb=" N VAL C 146 " pdb=" CA VAL C 146 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.41e+00 bond pdb=" N TYR m 39 " pdb=" CA TYR m 39 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.89e+00 ... (remaining 27472 not shown) Histogram of bond angle deviations from ideal: 96.37 - 104.15: 772 104.15 - 111.92: 13622 111.92 - 119.70: 9995 119.70 - 127.48: 13058 127.48 - 135.25: 447 Bond angle restraints: 37894 Sorted by residual: angle pdb=" C VAL l 15 " pdb=" N GLN l 16 " pdb=" CA GLN l 16 " ideal model delta sigma weight residual 121.76 135.25 -13.49 1.74e+00 3.30e-01 6.01e+01 angle pdb=" N CYS C 144 " pdb=" CA CYS C 144 " pdb=" CB CYS C 144 " ideal model delta sigma weight residual 109.94 120.47 -10.53 1.49e+00 4.50e-01 4.99e+01 angle pdb=" N LEU h 10 " pdb=" CA LEU h 10 " pdb=" C LEU h 10 " ideal model delta sigma weight residual 112.54 105.44 7.10 1.22e+00 6.72e-01 3.38e+01 angle pdb=" CA ILE A 867 " pdb=" CB ILE A 867 " pdb=" CG1 ILE A 867 " ideal model delta sigma weight residual 110.40 119.73 -9.33 1.70e+00 3.46e-01 3.01e+01 angle pdb=" C CYS C 144 " pdb=" CA CYS C 144 " pdb=" CB CYS C 144 " ideal model delta sigma weight residual 110.81 102.51 8.30 1.60e+00 3.91e-01 2.69e+01 ... (remaining 37889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 15840 35.12 - 70.24: 636 70.24 - 105.36: 57 105.36 - 140.48: 3 140.48 - 175.59: 8 Dihedral angle restraints: 16544 sinusoidal: 6871 harmonic: 9673 Sorted by residual: dihedral pdb=" O4' C 5 38 " pdb=" C1' C 5 38 " pdb=" N1 C 5 38 " pdb=" C2 C 5 38 " ideal model delta sinusoidal sigma weight residual -128.00 46.88 -174.88 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U 5 22 " pdb=" C1' U 5 22 " pdb=" N1 U 5 22 " pdb=" C2 U 5 22 " ideal model delta sinusoidal sigma weight residual 232.00 65.38 166.62 1 1.70e+01 3.46e-03 6.55e+01 dihedral pdb=" O4' C 5 71 " pdb=" C1' C 5 71 " pdb=" N1 C 5 71 " pdb=" C2 C 5 71 " ideal model delta sinusoidal sigma weight residual 232.00 71.13 160.87 1 1.70e+01 3.46e-03 6.46e+01 ... (remaining 16541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3952 0.075 - 0.150: 421 0.150 - 0.225: 19 0.225 - 0.300: 2 0.300 - 0.375: 1 Chirality restraints: 4395 Sorted by residual: chirality pdb=" CA THR C 143 " pdb=" N THR C 143 " pdb=" C THR C 143 " pdb=" CB THR C 143 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA MET j 99 " pdb=" N MET j 99 " pdb=" C MET j 99 " pdb=" CB MET j 99 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' GTP C1001 " pdb=" C2' GTP C1001 " pdb=" C4' GTP C1001 " pdb=" O3' GTP C1001 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 4392 not shown) Planarity restraints: 4549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 5 57 " -0.055 2.00e-02 2.50e+03 2.45e-02 1.80e+01 pdb=" N9 G 5 57 " 0.060 2.00e-02 2.50e+03 pdb=" C8 G 5 57 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 5 57 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 5 57 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 5 57 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G 5 57 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G 5 57 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G 5 57 " 0.012 2.00e-02 2.50e+03 pdb=" N2 G 5 57 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 5 57 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G 5 57 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1342 " -0.030 2.00e-02 2.50e+03 2.67e-02 1.79e+01 pdb=" CG TRP A1342 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A1342 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A1342 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A1342 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A1342 " 0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP A1342 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1342 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1342 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A1342 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1482 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" CD GLU A1482 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU A1482 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU A1482 " -0.021 2.00e-02 2.50e+03 ... (remaining 4546 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 325 2.62 - 3.19: 23539 3.19 - 3.76: 43132 3.76 - 4.33: 58360 4.33 - 4.90: 93515 Nonbonded interactions: 218871 Sorted by model distance: nonbonded pdb=" O MET A1622 " pdb=" OH TYR A1687 " model vdw 2.047 3.040 nonbonded pdb=" OH TYR A1660 " pdb=" O ASN A1717 " model vdw 2.093 3.040 nonbonded pdb=" OG SER A1625 " pdb=" OD2 ASP A1663 " model vdw 2.136 3.040 nonbonded pdb=" O2' G 5 57 " pdb=" O5' U 5 58 " model vdw 2.161 3.040 nonbonded pdb=" O LEU A1536 " pdb=" OG SER A1539 " model vdw 2.179 3.040 ... (remaining 218866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.160 Check model and map are aligned: 0.180 Set scattering table: 0.280 Process input model: 89.180 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.004 0.066 27477 Z= 0.247 Angle : 0.728 13.492 37894 Z= 0.392 Chirality : 0.045 0.375 4395 Planarity : 0.005 0.104 4549 Dihedral : 18.346 175.595 10265 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 2.18 % Allowed : 21.88 % Favored : 75.94 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.78 % 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: 0.07 (0.15), residues: 3267 helix: 1.19 (0.15), residues: 1231 sheet: -0.27 (0.23), residues: 470 loop : -0.74 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A1342 HIS 0.014 0.001 HIS A1024 PHE 0.023 0.002 PHE C 717 TYR 0.021 0.002 TYR A 783 ARG 0.014 0.001 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 185 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 39 residues processed: 228 average time/residue: 0.3722 time to fit residues: 142.1914 Evaluate side-chains 221 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1426 ASP Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 chunk 171 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 101 optimal weight: 0.0070 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1610 GLN C 139 HIS C 335 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 27477 Z= 0.222 Angle : 0.584 10.179 37894 Z= 0.303 Chirality : 0.043 0.207 4395 Planarity : 0.004 0.052 4549 Dihedral : 16.283 175.011 5227 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 3.07 % Allowed : 18.81 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.45 (0.15), residues: 3267 helix: 1.53 (0.15), residues: 1270 sheet: -0.29 (0.23), residues: 500 loop : -0.50 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1342 HIS 0.005 0.001 HIS A1712 PHE 0.019 0.001 PHE A1597 TYR 0.017 0.001 TYR A1008 ARG 0.006 0.000 ARG A1090 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 200 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 981 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8611 (m-10) REVERT: A 1049 ASP cc_start: 0.8668 (m-30) cc_final: 0.8455 (m-30) REVERT: A 1622 MET cc_start: 0.8087 (mpt) cc_final: 0.7845 (mpt) REVERT: A 1709 TYR cc_start: 0.7155 (m-80) cc_final: 0.6864 (m-80) REVERT: D 275 GLU cc_start: 0.8243 (mp0) cc_final: 0.7956 (tt0) REVERT: C 147 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8186 (p0) REVERT: C 338 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8861 (mm-30) REVERT: C 807 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7852 (tp40) outliers start: 69 outliers final: 33 residues processed: 253 average time/residue: 0.3816 time to fit residues: 159.7737 Evaluate side-chains 219 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 0.0870 chunk 207 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 0.0070 chunk 330 optimal weight: 50.0000 chunk 272 optimal weight: 2.9990 chunk 303 optimal weight: 0.0970 chunk 104 optimal weight: 7.9990 chunk 245 optimal weight: 0.8980 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A1424 GLN ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 27477 Z= 0.152 Angle : 0.545 12.745 37894 Z= 0.276 Chirality : 0.041 0.213 4395 Planarity : 0.004 0.052 4549 Dihedral : 16.044 178.408 5189 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.18 % Rotamer: Outliers : 2.80 % Allowed : 19.39 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.65 (0.15), residues: 3267 helix: 1.72 (0.15), residues: 1276 sheet: -0.10 (0.24), residues: 481 loop : -0.47 (0.17), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1342 HIS 0.004 0.001 HIS A1712 PHE 0.019 0.001 PHE A1597 TYR 0.027 0.001 TYR F 107 ARG 0.012 0.000 ARG A1401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 201 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8514 (m-10) REVERT: A 1049 ASP cc_start: 0.8757 (m-30) cc_final: 0.8554 (m-30) REVERT: A 1067 MET cc_start: 0.8644 (tpt) cc_final: 0.8280 (ppp) REVERT: A 1282 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7556 (mm-40) REVERT: A 1401 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6598 (ptp-170) REVERT: A 1597 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.7211 (t80) REVERT: A 1709 TYR cc_start: 0.7151 (m-80) cc_final: 0.6939 (m-80) REVERT: D 275 GLU cc_start: 0.8232 (mp0) cc_final: 0.7890 (tt0) REVERT: C 338 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8835 (mm-30) REVERT: C 822 MET cc_start: 0.8370 (mmt) cc_final: 0.8000 (mmm) outliers start: 63 outliers final: 32 residues processed: 249 average time/residue: 0.3560 time to fit residues: 146.4676 Evaluate side-chains 226 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1282 GLN Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1401 ARG Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 30.0000 chunk 229 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 306 optimal weight: 40.0000 chunk 324 optimal weight: 50.0000 chunk 160 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 87 optimal weight: 0.0070 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 834 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 GLN ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 27477 Z= 0.223 Angle : 0.539 9.122 37894 Z= 0.276 Chirality : 0.042 0.217 4395 Planarity : 0.004 0.055 4549 Dihedral : 15.940 179.860 5180 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 3.20 % Allowed : 18.63 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.80 (0.15), residues: 3267 helix: 1.85 (0.15), residues: 1269 sheet: -0.10 (0.24), residues: 489 loop : -0.35 (0.17), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1342 HIS 0.005 0.001 HIS C 928 PHE 0.017 0.001 PHE A1597 TYR 0.018 0.001 TYR F 107 ARG 0.006 0.000 ARG A 934 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 188 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 219 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8163 (mm-40) REVERT: A 474 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8739 (mtt-85) REVERT: A 934 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.8161 (mtm-85) REVERT: A 981 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8630 (m-10) REVERT: A 1049 ASP cc_start: 0.8737 (m-30) cc_final: 0.8474 (m-30) REVERT: A 1067 MET cc_start: 0.8687 (tpt) cc_final: 0.8316 (ppp) REVERT: A 1307 MET cc_start: 0.7273 (pmm) cc_final: 0.6541 (pmm) REVERT: A 1310 ARG cc_start: 0.8746 (ptm-80) cc_final: 0.8383 (ptm-80) REVERT: A 1597 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7333 (t80) REVERT: D 245 LYS cc_start: 0.8220 (mptt) cc_final: 0.7659 (mtpt) REVERT: D 275 GLU cc_start: 0.8218 (mp0) cc_final: 0.7872 (tt0) REVERT: C 338 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8816 (mm-30) REVERT: C 807 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7797 (tp40) outliers start: 72 outliers final: 38 residues processed: 244 average time/residue: 0.3558 time to fit residues: 144.8995 Evaluate side-chains 228 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 674 CYS Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.9990 chunk 184 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 241 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 277 optimal weight: 0.0770 chunk 224 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 291 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1056 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1554 GLN ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 27477 Z= 0.258 Angle : 0.548 9.169 37894 Z= 0.281 Chirality : 0.042 0.221 4395 Planarity : 0.004 0.055 4549 Dihedral : 15.890 176.514 5179 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 2.93 % Allowed : 18.85 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.84 (0.15), residues: 3267 helix: 1.84 (0.15), residues: 1279 sheet: -0.06 (0.24), residues: 493 loop : -0.31 (0.17), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1342 HIS 0.004 0.001 HIS C 928 PHE 0.020 0.001 PHE A1099 TYR 0.017 0.001 TYR F 107 ARG 0.003 0.000 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 189 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7333 (ttm170) REVERT: F 219 GLN cc_start: 0.8559 (tp40) cc_final: 0.8249 (mm-40) REVERT: A 474 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8701 (mtt-85) REVERT: A 981 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8643 (m-10) REVERT: A 1049 ASP cc_start: 0.8738 (m-30) cc_final: 0.8473 (m-30) REVERT: A 1067 MET cc_start: 0.8704 (tpt) cc_final: 0.8217 (ppp) REVERT: A 1310 ARG cc_start: 0.8671 (ptm-80) cc_final: 0.8336 (ptm-80) REVERT: A 1597 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7273 (t80) REVERT: D 245 LYS cc_start: 0.8261 (mptt) cc_final: 0.7653 (mtpt) REVERT: D 275 GLU cc_start: 0.8228 (mp0) cc_final: 0.7886 (tt0) REVERT: C 176 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: C 338 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8814 (mm-30) REVERT: C 793 ASP cc_start: 0.7827 (t0) cc_final: 0.7048 (p0) REVERT: C 807 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7826 (tp40) REVERT: C 822 MET cc_start: 0.8774 (mmm) cc_final: 0.8506 (mmm) outliers start: 66 outliers final: 40 residues processed: 242 average time/residue: 0.3761 time to fit residues: 151.4287 Evaluate side-chains 227 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 180 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 3.9990 chunk 292 optimal weight: 50.0000 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 325 optimal weight: 40.0000 chunk 269 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 107 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 27477 Z= 0.358 Angle : 0.585 9.810 37894 Z= 0.301 Chirality : 0.044 0.239 4395 Planarity : 0.004 0.056 4549 Dihedral : 15.881 175.164 5179 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 3.29 % Allowed : 18.81 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.76 (0.15), residues: 3267 helix: 1.79 (0.15), residues: 1274 sheet: -0.12 (0.24), residues: 493 loop : -0.35 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1342 HIS 0.006 0.001 HIS C 928 PHE 0.021 0.002 PHE A1099 TYR 0.016 0.002 TYR A 431 ARG 0.015 0.000 ARG A1354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 180 time to evaluate : 2.881 Fit side-chains revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7409 (ttm170) REVERT: F 198 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7425 (tpt-90) REVERT: F 219 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8257 (mm-40) REVERT: A 86 ARG cc_start: 0.7929 (ttt180) cc_final: 0.7629 (tpp80) REVERT: A 297 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8802 (p0) REVERT: A 474 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8783 (mtt-85) REVERT: A 934 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8188 (mtm-85) REVERT: A 981 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8721 (m-10) REVERT: A 1049 ASP cc_start: 0.8692 (m-30) cc_final: 0.8431 (m-30) REVERT: A 1123 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8455 (mp0) REVERT: A 1342 TRP cc_start: 0.6313 (p90) cc_final: 0.6056 (p-90) REVERT: A 1597 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7292 (t80) REVERT: D 245 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7693 (mtpt) REVERT: D 275 GLU cc_start: 0.8261 (mp0) cc_final: 0.7934 (tt0) REVERT: C 176 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: C 338 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8821 (mm-30) REVERT: C 793 ASP cc_start: 0.7868 (t0) cc_final: 0.7100 (p0) REVERT: C 807 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7807 (tp40) REVERT: C 822 MET cc_start: 0.8837 (mmm) cc_final: 0.8409 (mmm) outliers start: 74 outliers final: 48 residues processed: 241 average time/residue: 0.3643 time to fit residues: 145.2381 Evaluate side-chains 236 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 178 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 50.0000 chunk 36 optimal weight: 0.0980 chunk 185 optimal weight: 30.0000 chunk 237 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 273 optimal weight: 0.3980 chunk 181 optimal weight: 4.9990 chunk 323 optimal weight: 50.0000 chunk 202 optimal weight: 0.9980 chunk 197 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27477 Z= 0.231 Angle : 0.545 9.075 37894 Z= 0.279 Chirality : 0.042 0.266 4395 Planarity : 0.004 0.053 4549 Dihedral : 15.805 175.540 5179 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 2.93 % Allowed : 19.16 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.83 (0.15), residues: 3267 helix: 1.88 (0.15), residues: 1275 sheet: -0.07 (0.24), residues: 505 loop : -0.35 (0.17), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1342 HIS 0.004 0.001 HIS C 928 PHE 0.018 0.001 PHE A1099 TYR 0.013 0.001 TYR A 431 ARG 0.005 0.000 ARG A 934 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 181 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7391 (ttm170) REVERT: F 219 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8340 (mm110) REVERT: A 297 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8818 (p0) REVERT: A 474 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8756 (mtt-85) REVERT: A 981 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8631 (m-10) REVERT: A 1049 ASP cc_start: 0.8707 (m-30) cc_final: 0.8448 (m-30) REVERT: A 1282 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7916 (mm-40) REVERT: A 1310 ARG cc_start: 0.8533 (ptm-80) cc_final: 0.8322 (ptm-80) REVERT: A 1342 TRP cc_start: 0.6532 (p90) cc_final: 0.6129 (p-90) REVERT: A 1597 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7302 (t80) REVERT: D 245 LYS cc_start: 0.8309 (mptt) cc_final: 0.7666 (mtpt) REVERT: D 275 GLU cc_start: 0.8197 (mp0) cc_final: 0.7841 (tt0) REVERT: C 176 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: C 338 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8809 (mm-30) REVERT: C 793 ASP cc_start: 0.7869 (t0) cc_final: 0.7090 (p0) REVERT: C 807 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7733 (tp40) REVERT: C 822 MET cc_start: 0.8830 (mmm) cc_final: 0.8454 (mmm) outliers start: 66 outliers final: 44 residues processed: 237 average time/residue: 0.3512 time to fit residues: 138.7355 Evaluate side-chains 232 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1282 GLN Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27477 Z= 0.204 Angle : 0.533 10.122 37894 Z= 0.272 Chirality : 0.042 0.235 4395 Planarity : 0.004 0.053 4549 Dihedral : 15.716 177.240 5179 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 2.67 % Allowed : 19.25 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.97 (0.15), residues: 3267 helix: 1.96 (0.15), residues: 1273 sheet: 0.03 (0.24), residues: 510 loop : -0.25 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1342 HIS 0.004 0.001 HIS C 928 PHE 0.016 0.001 PHE A1099 TYR 0.012 0.001 TYR A 431 ARG 0.007 0.000 ARG A 934 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7405 (ttm170) REVERT: A 297 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8873 (p0) REVERT: A 474 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8909 (mtt-85) REVERT: A 981 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8625 (m-10) REVERT: A 1049 ASP cc_start: 0.8701 (m-30) cc_final: 0.8441 (m-30) REVERT: A 1189 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5315 (ttt) REVERT: A 1282 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7788 (mm-40) REVERT: A 1310 ARG cc_start: 0.8556 (ptm-80) cc_final: 0.8342 (ptm-80) REVERT: A 1597 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7330 (t80) REVERT: D 245 LYS cc_start: 0.8309 (mptt) cc_final: 0.7673 (mtpt) REVERT: D 275 GLU cc_start: 0.8185 (mp0) cc_final: 0.7835 (tt0) REVERT: C 176 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: C 338 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8796 (mm-30) REVERT: C 793 ASP cc_start: 0.7814 (t0) cc_final: 0.7218 (p0) REVERT: C 807 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: C 822 MET cc_start: 0.8816 (mmm) cc_final: 0.8451 (mmm) outliers start: 60 outliers final: 41 residues processed: 229 average time/residue: 0.3441 time to fit residues: 132.0064 Evaluate side-chains 225 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 174 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1282 GLN Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 50.0000 chunk 310 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 301 optimal weight: 0.0870 chunk 181 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 272 optimal weight: 0.7980 chunk 285 optimal weight: 40.0000 chunk 300 optimal weight: 9.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 27477 Z= 0.454 Angle : 0.643 12.516 37894 Z= 0.329 Chirality : 0.046 0.280 4395 Planarity : 0.004 0.056 4549 Dihedral : 15.831 175.152 5179 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 2.62 % Allowed : 19.52 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.72 (0.15), residues: 3267 helix: 1.74 (0.15), residues: 1277 sheet: -0.09 (0.23), residues: 520 loop : -0.37 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 637 HIS 0.007 0.001 HIS C 928 PHE 0.025 0.002 PHE A1099 TYR 0.025 0.002 TYR C 167 ARG 0.004 0.001 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 172 time to evaluate : 2.875 Fit side-chains revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7400 (ttm170) REVERT: F 198 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7297 (mmm160) REVERT: A 297 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8715 (p0) REVERT: A 474 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8816 (mtt-85) REVERT: A 981 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8780 (m-10) REVERT: A 1123 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8472 (mp0) REVERT: A 1189 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5548 (ttt) REVERT: A 1310 ARG cc_start: 0.8446 (ptm-80) cc_final: 0.8224 (ptm-80) REVERT: A 1591 MET cc_start: 0.8538 (tmm) cc_final: 0.8336 (tpt) REVERT: D 245 LYS cc_start: 0.8397 (mptt) cc_final: 0.7778 (mtpt) REVERT: D 275 GLU cc_start: 0.8188 (mp0) cc_final: 0.7861 (tt0) REVERT: C 176 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: C 338 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8825 (mm-30) REVERT: C 793 ASP cc_start: 0.7883 (t0) cc_final: 0.7366 (p0) REVERT: C 807 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7630 (tt0) outliers start: 59 outliers final: 40 residues processed: 222 average time/residue: 0.3627 time to fit residues: 136.3744 Evaluate side-chains 219 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 170 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.5980 chunk 319 optimal weight: 50.0000 chunk 194 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 221 optimal weight: 0.6980 chunk 334 optimal weight: 30.0000 chunk 308 optimal weight: 40.0000 chunk 266 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 205 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1460 HIS ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27477 Z= 0.200 Angle : 0.550 10.335 37894 Z= 0.279 Chirality : 0.042 0.301 4395 Planarity : 0.004 0.054 4549 Dihedral : 15.732 176.484 5179 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 1.96 % Allowed : 20.10 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.93 (0.15), residues: 3267 helix: 1.94 (0.15), residues: 1270 sheet: -0.01 (0.24), residues: 517 loop : -0.27 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1342 HIS 0.004 0.001 HIS C 928 PHE 0.017 0.001 PHE A1099 TYR 0.016 0.001 TYR A1494 ARG 0.007 0.000 ARG F 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 176 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7464 (ttm170) REVERT: F 118 SER cc_start: 0.8984 (t) cc_final: 0.8572 (m) REVERT: F 198 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7311 (mmm160) REVERT: A 297 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8771 (p0) REVERT: A 474 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8950 (mtt-85) REVERT: A 981 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8607 (m-10) REVERT: A 1049 ASP cc_start: 0.8716 (m-30) cc_final: 0.8490 (m-30) REVERT: A 1067 MET cc_start: 0.8300 (tpp) cc_final: 0.7918 (tmm) REVERT: A 1123 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8441 (mp0) REVERT: A 1310 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.8269 (ptm-80) REVERT: A 1591 MET cc_start: 0.8604 (tmm) cc_final: 0.8394 (tpt) REVERT: D 245 LYS cc_start: 0.8338 (mptt) cc_final: 0.7713 (mtpt) REVERT: D 275 GLU cc_start: 0.8179 (mp0) cc_final: 0.7843 (tt0) REVERT: C 176 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: C 338 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8814 (mm-30) REVERT: C 793 ASP cc_start: 0.7853 (t0) cc_final: 0.7354 (p0) REVERT: C 807 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: C 822 MET cc_start: 0.8712 (mmm) cc_final: 0.8290 (mtt) outliers start: 44 outliers final: 34 residues processed: 215 average time/residue: 0.3817 time to fit residues: 137.9987 Evaluate side-chains 217 residues out of total 2972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1458 GLN Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1597 PHE Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 1.9990 chunk 283 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 274 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.108106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070534 restraints weight = 76825.737| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.45 r_work: 0.2958 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27477 Z= 0.279 Angle : 0.569 9.915 37894 Z= 0.289 Chirality : 0.043 0.308 4395 Planarity : 0.004 0.054 4549 Dihedral : 15.712 176.973 5179 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 2.13 % Allowed : 20.05 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % 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: 0.88 (0.15), residues: 3267 helix: 1.89 (0.15), residues: 1283 sheet: 0.02 (0.24), residues: 494 loop : -0.32 (0.17), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1342 HIS 0.005 0.001 HIS C 928 PHE 0.020 0.001 PHE A1099 TYR 0.019 0.001 TYR C 167 ARG 0.008 0.000 ARG F 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.12 seconds wall clock time: 97 minutes 29.91 seconds (5849.91 seconds total)