Starting phenix.real_space_refine on Mon Mar 18 13:27:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8l_27251/03_2024/8d8l_27251_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8l_27251/03_2024/8d8l_27251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8l_27251/03_2024/8d8l_27251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8l_27251/03_2024/8d8l_27251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8l_27251/03_2024/8d8l_27251_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8l_27251/03_2024/8d8l_27251_neut_updated.pdb" } resolution = 2.6 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= 0.022 sd= 0.970 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 1509 5.49 5 Mg 72 5.21 5 S 209 5.16 5 C 49374 2.51 5 N 15417 2.21 5 O 20422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 200": "OE1" <-> "OE2" Residue "0 GLU 310": "OE1" <-> "OE2" Residue "0 GLU 318": "OE1" <-> "OE2" Residue "0 PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 414": "OE1" <-> "OE2" Residue "0 TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 558": "OD1" <-> "OD2" Residue "5 PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 244": "OE1" <-> "OE2" Residue "5 TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 316": "OD1" <-> "OD2" Residue "C TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 68": "OE1" <-> "OE2" Residue "O GLU 85": "OE1" <-> "OE2" Residue "O GLU 158": "OE1" <-> "OE2" Residue "P ASP 70": "OD1" <-> "OD2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 67": "OD1" <-> "OD2" Residue "S GLU 75": "OE1" <-> "OE2" Residue "T PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 25": "OE1" <-> "OE2" Residue "U TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 62": "OD1" <-> "OD2" Residue "U ASP 164": "OD1" <-> "OD2" Residue "U GLU 195": "OE1" <-> "OE2" Residue "V ASP 31": "OD1" <-> "OD2" Residue "V ASP 70": "OD1" <-> "OD2" Residue "V ASP 72": "OD1" <-> "OD2" Residue "V GLU 133": "OE1" <-> "OE2" Residue "V GLU 146": "OE1" <-> "OE2" Residue "V ASP 150": "OD1" <-> "OD2" Residue "V GLU 171": "OE1" <-> "OE2" Residue "V TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 221": "OD1" <-> "OD2" Residue "V ASP 226": "OD1" <-> "OD2" Residue "W TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 169": "OD1" <-> "OD2" Residue "W GLU 309": "OE1" <-> "OE2" Residue "W PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 72": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 212": "OE1" <-> "OE2" Residue "Y ASP 239": "OD1" <-> "OD2" Residue "Y ASP 269": "OD1" <-> "OD2" Residue "Y ASP 310": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 296": "OD1" <-> "OD2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "2 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 76": "OE1" <-> "OE2" Residue "2 GLU 102": "OE1" <-> "OE2" Residue "3 TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 114": "OE1" <-> "OE2" Residue "3 ASP 131": "OD1" <-> "OD2" Residue "3 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 184": "OD1" <-> "OD2" Residue "3 ASP 192": "OD1" <-> "OD2" Residue "3 ASP 234": "OD1" <-> "OD2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 129": "OE1" <-> "OE2" Residue "4 ASP 166": "OD1" <-> "OD2" Residue "4 ASP 194": "OD1" <-> "OD2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "E ASP 138": "OD1" <-> "OD2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E ASP 221": "OD1" <-> "OD2" Residue "E ASP 268": "OD1" <-> "OD2" Residue "E TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "6 TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 183": "OE1" <-> "OE2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G ASP 207": "OD1" <-> "OD2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "8 ASP 101": "OD1" <-> "OD2" Residue "8 ASP 174": "OD1" <-> "OD2" Residue "8 GLU 229": "OE1" <-> "OE2" Residue "8 GLU 240": "OE1" <-> "OE2" Residue "8 TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 263": "OD1" <-> "OD2" Residue "8 TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 458": "OE1" <-> "OE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 117": "OD1" <-> "OD2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 260": "OE1" <-> "OE2" Residue "J TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "K TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 153": "OE1" <-> "OE2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K ASP 200": "OD1" <-> "OD2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 87007 Number of models: 1 Model: "" Number of chains: 41 Chain: "0" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3626 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 421} Chain breaks: 4 Chain: "5" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2199 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 13, 'TRANS': 256} Chain breaks: 2 Chain: "C" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 2018 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 237} Chain breaks: 5 Chain: "M" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "N" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 923 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "O" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1727 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 5, 'TRANS': 204} Chain breaks: 1 Chain: "P" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 919 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain breaks: 1 Chain: "Q" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1683 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 2, 'TRANS': 201} Chain breaks: 4 Chain: "R" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 738 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "S" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 595 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 7, 'TRANS': 67} Chain: "T" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 760 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "U" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1907 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "V" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1879 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "W" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3174 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain: "X" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "Y" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2208 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain breaks: 1 Chain: "Z" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 660 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain breaks: 1 Chain: "A" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1585 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 3 Chain: "B" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2085 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 16, 'TRANS': 249} Chain: "2" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 833 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "3" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1953 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2713 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 23, 'TRANS': 302} Chain breaks: 2 Chain: "4" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2182 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 12, 'TRANS': 258} Chain breaks: 2 Chain: "E" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2297 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 16, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "6" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2488 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Chain: "G" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1168 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "H" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1213 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "8" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3573 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 1 Chain: "I" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 199} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "a" Number of atoms: 31987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1506, 31987 Classifications: {'RNA': 1506} Modifications used: {'rna2p_pur': 135, 'rna2p_pyr': 105, 'rna3p_pur': 696, 'rna3p_pyr': 570} Link IDs: {'rna2p': 239, 'rna3p': 1266} Chain breaks: 11 Chain: "J" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1186 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 10, 'TRANS': 133} Chain breaks: 2 Chain: "K" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1121 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 1 Chain: "c" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 470 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'TRANS': 93} Chain breaks: 3 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'UNK:plan-1': 94} Unresolved non-hydrogen planarities: 94 Chain: "L" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 926 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 112} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Unusual residues: {' MG': 69} Classifications: {'undetermined': 69} Link IDs: {None: 68} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2256 SG CYS 0 400 149.357 139.533 131.463 1.00 8.23 S ATOM 2033 SG CYS 0 373 154.478 138.947 135.297 1.00 7.84 S ATOM 3068 SG CYS 0 513 151.264 144.392 135.365 1.00 8.19 S ATOM 2085 SG CYS 0 379 148.410 139.450 137.693 1.00 9.53 S Time building chain proxies: 34.53, per 1000 atoms: 0.40 Number of scatterers: 87007 At special positions: 0 Unit cell: (190.26, 224.084, 330.841, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 209 16.00 P 1509 15.00 Mg 72 11.99 O 20422 8.00 N 15417 7.00 C 49374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Z 40 " - pdb=" SG CYS Z 51 " distance=2.03 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: 33.56 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 701 " pdb="FE3 SF4 0 701 " - pdb=" SG CYS 0 513 " pdb="FE2 SF4 0 701 " - pdb=" SG CYS 0 373 " pdb="FE1 SF4 0 701 " - pdb=" SG CYS 0 400 " pdb="FE4 SF4 0 701 " - pdb=" SG CYS 0 379 " Number of angles added : 12 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12978 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 304 helices and 40 sheets defined 46.7% alpha, 8.9% beta 481 base pairs and 785 stacking pairs defined. Time for finding SS restraints: 33.99 Creating SS restraints... Processing helix chain '0' and resid 66 through 71 Processing helix chain '0' and resid 82 through 91 Processing helix chain '0' and resid 98 through 110 Processing helix chain '0' and resid 125 through 134 Processing helix chain '0' and resid 136 through 153 Processing helix chain '0' and resid 155 through 158 No H-bonds generated for 'chain '0' and resid 155 through 158' Processing helix chain '0' and resid 173 through 182 Processing helix chain '0' and resid 200 through 211 removed outlier: 3.549A pdb=" N ARG 0 204 " --> pdb=" O GLU 0 200 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG 0 211 " --> pdb=" O ILE 0 207 " (cutoff:3.500A) Processing helix chain '0' and resid 285 through 297 removed outlier: 3.868A pdb=" N VAL 0 289 " --> pdb=" O PHE 0 285 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP 0 290 " --> pdb=" O PRO 0 286 " (cutoff:3.500A) Processing helix chain '0' and resid 314 through 328 Processing helix chain '0' and resid 330 through 333 Processing helix chain '0' and resid 386 through 390 Processing helix chain '0' and resid 410 through 415 Processing helix chain '0' and resid 463 through 474 Processing helix chain '0' and resid 530 through 538 removed outlier: 3.760A pdb=" N LYS 0 538 " --> pdb=" O HIS 0 534 " (cutoff:3.500A) Processing helix chain '0' and resid 556 through 558 No H-bonds generated for 'chain '0' and resid 556 through 558' Processing helix chain '0' and resid 575 through 589 Processing helix chain '5' and resid 42 through 56 removed outlier: 3.917A pdb=" N ASP 5 49 " --> pdb=" O LYS 5 45 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 66 Proline residue: 5 63 - end of helix Processing helix chain '5' and resid 71 through 75 Processing helix chain '5' and resid 99 through 107 removed outlier: 3.783A pdb=" N ASN 5 103 " --> pdb=" O LYS 5 99 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP 5 104 " --> pdb=" O GLN 5 100 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE 5 105 " --> pdb=" O THR 5 101 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE 5 106 " --> pdb=" O LEU 5 102 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR 5 107 " --> pdb=" O ASN 5 103 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 99 through 107' Processing helix chain '5' and resid 116 through 124 Processing helix chain '5' and resid 131 through 136 Processing helix chain '5' and resid 139 through 151 Processing helix chain '5' and resid 156 through 173 removed outlier: 4.746A pdb=" N LYS 5 172 " --> pdb=" O HIS 5 168 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA 5 173 " --> pdb=" O LYS 5 169 " (cutoff:3.500A) Processing helix chain '5' and resid 185 through 199 removed outlier: 3.577A pdb=" N HIS 5 194 " --> pdb=" O MET 5 190 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS 5 199 " --> pdb=" O ARG 5 195 " (cutoff:3.500A) Processing helix chain '5' and resid 204 through 216 Processing helix chain '5' and resid 227 through 239 Processing helix chain '5' and resid 264 through 287 removed outlier: 5.409A pdb=" N GLY 5 276 " --> pdb=" O SER 5 272 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE 5 277 " --> pdb=" O LYS 5 273 " (cutoff:3.500A) Processing helix chain '5' and resid 290 through 292 No H-bonds generated for 'chain '5' and resid 290 through 292' Processing helix chain '5' and resid 296 through 307 removed outlier: 3.737A pdb=" N PHE 5 300 " --> pdb=" O GLU 5 296 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE 5 301 " --> pdb=" O LEU 5 297 " (cutoff:3.500A) Processing helix chain '5' and resid 314 through 326 removed outlier: 3.606A pdb=" N HIS 5 318 " --> pdb=" O PRO 5 314 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY 5 323 " --> pdb=" O LEU 5 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 59 Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 102 through 123 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 254 through 280 Processing helix chain 'C' and resid 302 through 305 No H-bonds generated for 'chain 'C' and resid 302 through 305' Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'M' and resid 16 through 23 removed outlier: 3.710A pdb=" N ALA M 21 " --> pdb=" O LYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 38 Processing helix chain 'M' and resid 47 through 49 No H-bonds generated for 'chain 'M' and resid 47 through 49' Processing helix chain 'M' and resid 52 through 64 Processing helix chain 'M' and resid 68 through 83 Processing helix chain 'N' and resid 19 through 46 removed outlier: 5.282A pdb=" N ILE N 36 " --> pdb=" O LYS N 32 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LEU N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 64 Processing helix chain 'N' and resid 67 through 69 No H-bonds generated for 'chain 'N' and resid 67 through 69' Processing helix chain 'N' and resid 71 through 73 No H-bonds generated for 'chain 'N' and resid 71 through 73' Processing helix chain 'N' and resid 95 through 104 Processing helix chain 'O' and resid 35 through 59 Processing helix chain 'O' and resid 74 through 83 Processing helix chain 'O' and resid 95 through 111 Processing helix chain 'O' and resid 129 through 142 Processing helix chain 'O' and resid 144 through 146 No H-bonds generated for 'chain 'O' and resid 144 through 146' Processing helix chain 'O' and resid 149 through 164 Processing helix chain 'O' and resid 174 through 194 Processing helix chain 'O' and resid 199 through 222 Processing helix chain 'O' and resid 224 through 234 Processing helix chain 'O' and resid 238 through 242 Processing helix chain 'O' and resid 249 through 254 Processing helix chain 'P' and resid 52 through 57 Processing helix chain 'P' and resid 69 through 78 Processing helix chain 'P' and resid 84 through 92 Processing helix chain 'P' and resid 98 through 100 No H-bonds generated for 'chain 'P' and resid 98 through 100' Processing helix chain 'Q' and resid 81 through 116 removed outlier: 3.701A pdb=" N GLN Q 93 " --> pdb=" O GLU Q 89 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU Q 94 " --> pdb=" O SER Q 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA Q 97 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU Q 99 " --> pdb=" O SER Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 133 Processing helix chain 'Q' and resid 143 through 148 Processing helix chain 'Q' and resid 161 through 164 No H-bonds generated for 'chain 'Q' and resid 161 through 164' Processing helix chain 'Q' and resid 168 through 195 Processing helix chain 'Q' and resid 197 through 206 removed outlier: 3.703A pdb=" N ASP Q 201 " --> pdb=" O ASP Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 219 through 231 Processing helix chain 'R' and resid 43 through 45 No H-bonds generated for 'chain 'R' and resid 43 through 45' Processing helix chain 'R' and resid 57 through 59 No H-bonds generated for 'chain 'R' and resid 57 through 59' Processing helix chain 'R' and resid 62 through 70 Processing helix chain 'R' and resid 89 through 92 Processing helix chain 'R' and resid 96 through 99 No H-bonds generated for 'chain 'R' and resid 96 through 99' Processing helix chain 'R' and resid 112 through 115 No H-bonds generated for 'chain 'R' and resid 112 through 115' Processing helix chain 'R' and resid 119 through 134 Processing helix chain 'S' and resid 12 through 14 No H-bonds generated for 'chain 'S' and resid 12 through 14' Processing helix chain 'S' and resid 24 through 28 Processing helix chain 'S' and resid 44 through 46 No H-bonds generated for 'chain 'S' and resid 44 through 46' Processing helix chain 'S' and resid 73 through 76 Processing helix chain 'T' and resid 87 through 99 removed outlier: 4.478A pdb=" N GLU T 94 " --> pdb=" O ARG T 90 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN T 95 " --> pdb=" O SER T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 126 Processing helix chain 'T' and resid 129 through 135 Processing helix chain 'T' and resid 142 through 175 Processing helix chain 'U' and resid 10 through 20 Processing helix chain 'U' and resid 30 through 35 Processing helix chain 'U' and resid 63 through 65 No H-bonds generated for 'chain 'U' and resid 63 through 65' Processing helix chain 'U' and resid 88 through 92 removed outlier: 3.730A pdb=" N TYR U 92 " --> pdb=" O VAL U 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 88 through 92' Processing helix chain 'U' and resid 100 through 111 removed outlier: 3.552A pdb=" N TYR U 109 " --> pdb=" O ARG U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 117 Processing helix chain 'U' and resid 127 through 129 No H-bonds generated for 'chain 'U' and resid 127 through 129' Processing helix chain 'U' and resid 146 through 158 Processing helix chain 'U' and resid 165 through 197 Processing helix chain 'U' and resid 205 through 232 removed outlier: 3.828A pdb=" N VAL U 219 " --> pdb=" O GLU U 215 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 8 Processing helix chain 'V' and resid 30 through 36 Processing helix chain 'V' and resid 43 through 45 No H-bonds generated for 'chain 'V' and resid 43 through 45' Processing helix chain 'V' and resid 71 through 78 Processing helix chain 'V' and resid 92 through 142 removed outlier: 3.686A pdb=" N LYS V 134 " --> pdb=" O LYS V 130 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU V 137 " --> pdb=" O GLU V 133 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 152 Processing helix chain 'V' and resid 157 through 161 Processing helix chain 'V' and resid 170 through 208 removed outlier: 3.731A pdb=" N VAL V 205 " --> pdb=" O ASN V 201 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN V 207 " --> pdb=" O TYR V 203 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU V 208 " --> pdb=" O HIS V 204 " (cutoff:3.500A) Processing helix chain 'V' and resid 213 through 225 Processing helix chain 'W' and resid 60 through 66 Processing helix chain 'W' and resid 69 through 72 removed outlier: 3.781A pdb=" N THR W 72 " --> pdb=" O LEU W 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 69 through 72' Processing helix chain 'W' and resid 86 through 89 No H-bonds generated for 'chain 'W' and resid 86 through 89' Processing helix chain 'W' and resid 98 through 107 Processing helix chain 'W' and resid 116 through 118 No H-bonds generated for 'chain 'W' and resid 116 through 118' Processing helix chain 'W' and resid 131 through 140 Processing helix chain 'W' and resid 156 through 170 Processing helix chain 'W' and resid 202 through 215 Processing helix chain 'W' and resid 218 through 222 Processing helix chain 'W' and resid 255 through 260 Processing helix chain 'W' and resid 265 through 281 removed outlier: 4.315A pdb=" N GLY W 269 " --> pdb=" O PRO W 265 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LYS W 270 " --> pdb=" O HIS W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 294 through 298 Processing helix chain 'W' and resid 315 through 317 No H-bonds generated for 'chain 'W' and resid 315 through 317' Processing helix chain 'W' and resid 319 through 329 Processing helix chain 'W' and resid 353 through 358 Processing helix chain 'W' and resid 370 through 372 No H-bonds generated for 'chain 'W' and resid 370 through 372' Processing helix chain 'W' and resid 375 through 383 Processing helix chain 'W' and resid 396 through 408 Processing helix chain 'W' and resid 414 through 417 No H-bonds generated for 'chain 'W' and resid 414 through 417' Processing helix chain 'W' and resid 422 through 432 Processing helix chain 'W' and resid 438 through 446 Processing helix chain 'X' and resid 5 through 19 Processing helix chain 'X' and resid 32 through 36 Processing helix chain 'X' and resid 41 through 45 Processing helix chain 'X' and resid 56 through 62 removed outlier: 4.145A pdb=" N LYS X 60 " --> pdb=" O PHE X 56 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 85 Processing helix chain 'Y' and resid 50 through 52 No H-bonds generated for 'chain 'Y' and resid 50 through 52' Processing helix chain 'Y' and resid 54 through 57 Processing helix chain 'Y' and resid 62 through 79 removed outlier: 6.889A pdb=" N SER Y 78 " --> pdb=" O ALA Y 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU Y 79 " --> pdb=" O ARG Y 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 95 removed outlier: 4.556A pdb=" N GLU Y 95 " --> pdb=" O LEU Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 117 removed outlier: 7.461A pdb=" N GLU Y 112 " --> pdb=" O TYR Y 108 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLN Y 113 " --> pdb=" O HIS Y 109 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 160 removed outlier: 3.552A pdb=" N LEU Y 144 " --> pdb=" O GLN Y 140 " (cutoff:3.500A) Processing helix chain 'Y' and resid 163 through 168 Processing helix chain 'Y' and resid 195 through 198 removed outlier: 3.570A pdb=" N ARG Y 198 " --> pdb=" O PRO Y 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 195 through 198' Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Y' and resid 213 through 226 removed outlier: 6.347A pdb=" N SER Y 225 " --> pdb=" O ILE Y 221 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG Y 226 " --> pdb=" O LEU Y 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 244 through 263 Processing helix chain 'Y' and resid 278 through 286 removed outlier: 3.758A pdb=" N ARG Y 286 " --> pdb=" O ALA Y 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 296 through 298 No H-bonds generated for 'chain 'Y' and resid 296 through 298' Processing helix chain 'Y' and resid 301 through 303 No H-bonds generated for 'chain 'Y' and resid 301 through 303' Processing helix chain 'Y' and resid 311 through 316 Processing helix chain 'Z' and resid 29 through 44 Processing helix chain 'Z' and resid 49 through 61 removed outlier: 3.616A pdb=" N ALA Z 52 " --> pdb=" O PRO Z 49 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY Z 53 " --> pdb=" O LYS Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 89 removed outlier: 5.084A pdb=" N ASP Z 87 " --> pdb=" O ALA Z 83 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ARG Z 88 " --> pdb=" O ARG Z 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 11 through 14 No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.754A pdb=" N ARG A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.695A pdb=" N ASN A 86 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 88 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 6.753A pdb=" N ASP A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N PHE A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ARG A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N MET A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.520A pdb=" N PHE B 175 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.921A pdb=" N SER B 208 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 283 through 286 No H-bonds generated for 'chain 'B' and resid 283 through 286' Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 366 through 392 Processing helix chain '2' and resid 41 through 48 Processing helix chain '2' and resid 53 through 56 Processing helix chain '2' and resid 63 through 68 Processing helix chain '2' and resid 71 through 77 Processing helix chain '2' and resid 81 through 95 Processing helix chain '2' and resid 114 through 127 removed outlier: 5.190A pdb=" N LYS 2 118 " --> pdb=" O ARG 2 115 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA 2 119 " --> pdb=" O LYS 2 116 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS 2 125 " --> pdb=" O ALA 2 122 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA 2 126 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 23 Processing helix chain '3' and resid 31 through 37 Processing helix chain '3' and resid 41 through 53 Processing helix chain '3' and resid 57 through 60 Processing helix chain '3' and resid 63 through 70 Processing helix chain '3' and resid 74 through 96 removed outlier: 4.810A pdb=" N ASN 3 78 " --> pdb=" O LEU 3 75 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE 3 86 " --> pdb=" O ALA 3 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE 3 92 " --> pdb=" O ASN 3 89 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL 3 93 " --> pdb=" O HIS 3 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU 3 94 " --> pdb=" O LEU 3 91 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 126 Processing helix chain '3' and resid 132 through 146 Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 191 through 206 Processing helix chain '3' and resid 228 through 231 No H-bonds generated for 'chain '3' and resid 228 through 231' Processing helix chain '3' and resid 240 through 250 Processing helix chain '3' and resid 253 through 258 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 41 through 55 Processing helix chain 'D' and resid 62 through 68 Processing helix chain 'D' and resid 93 through 103 removed outlier: 4.317A pdb=" N PHE D 98 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL D 100 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 103 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 154 through 161 Processing helix chain 'D' and resid 168 through 191 Processing helix chain 'D' and resid 193 through 206 Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.514A pdb=" N ALA D 377 " --> pdb=" O PRO D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'D' and resid 471 through 482 Processing helix chain '4' and resid 34 through 40 Processing helix chain '4' and resid 42 through 55 removed outlier: 3.886A pdb=" N ASP 4 54 " --> pdb=" O ALA 4 50 " (cutoff:3.500A) Processing helix chain '4' and resid 58 through 61 No H-bonds generated for 'chain '4' and resid 58 through 61' Processing helix chain '4' and resid 64 through 70 Processing helix chain '4' and resid 78 through 95 Processing helix chain '4' and resid 113 through 117 Processing helix chain '4' and resid 131 through 133 No H-bonds generated for 'chain '4' and resid 131 through 133' Processing helix chain '4' and resid 136 through 146 Processing helix chain '4' and resid 149 through 161 Processing helix chain '4' and resid 215 through 229 Processing helix chain '4' and resid 245 through 257 Processing helix chain '4' and resid 277 through 284 removed outlier: 5.406A pdb=" N THR 4 282 " --> pdb=" O LYS 4 278 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP 4 283 " --> pdb=" O THR 4 279 " (cutoff:3.500A) Processing helix chain '4' and resid 289 through 299 Processing helix chain '4' and resid 302 through 308 Processing helix chain 'E' and resid 18 through 23 removed outlier: 4.014A pdb=" N ARG E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 39 removed outlier: 4.574A pdb=" N LYS E 31 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'E' and resid 137 through 143 Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 244 through 253 Processing helix chain 'E' and resid 268 through 281 removed outlier: 3.673A pdb=" N ILE E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 293 Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'F' and resid 14 through 35 Proline residue: F 17 - end of helix removed outlier: 3.951A pdb=" N GLU F 20 " --> pdb=" O PRO F 17 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 22 " --> pdb=" O LEU F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 110 through 115 Processing helix chain 'F' and resid 120 through 124 Processing helix chain '6' and resid 53 through 62 Processing helix chain '6' and resid 132 through 134 No H-bonds generated for 'chain '6' and resid 132 through 134' Processing helix chain '6' and resid 151 through 162 Processing helix chain '6' and resid 168 through 175 Processing helix chain '6' and resid 179 through 197 Processing helix chain '6' and resid 203 through 213 Processing helix chain '6' and resid 237 through 240 No H-bonds generated for 'chain '6' and resid 237 through 240' Processing helix chain '6' and resid 255 through 261 Processing helix chain '6' and resid 267 through 275 removed outlier: 3.590A pdb=" N LEU 6 271 " --> pdb=" O ALA 6 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 103 removed outlier: 4.212A pdb=" N SER G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 127 through 145 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 185 through 202 removed outlier: 3.765A pdb=" N GLN G 202 " --> pdb=" O GLN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 220 Processing helix chain 'G' and resid 225 through 239 Processing helix chain 'G' and resid 241 through 243 No H-bonds generated for 'chain 'G' and resid 241 through 243' Processing helix chain 'H' and resid 3 through 19 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 138 through 143 Processing helix chain '8' and resid 63 through 78 removed outlier: 3.799A pdb=" N LYS 8 78 " --> pdb=" O ASN 8 74 " (cutoff:3.500A) Processing helix chain '8' and resid 102 through 110 Processing helix chain '8' and resid 114 through 132 Processing helix chain '8' and resid 149 through 155 Processing helix chain '8' and resid 183 through 190 Proline residue: 8 188 - end of helix Processing helix chain '8' and resid 199 through 207 Processing helix chain '8' and resid 213 through 218 Processing helix chain '8' and resid 228 through 240 removed outlier: 4.429A pdb=" N ASP 8 232 " --> pdb=" O SER 8 228 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA 8 233 " --> pdb=" O GLU 8 229 " (cutoff:3.500A) Processing helix chain '8' and resid 252 through 265 removed outlier: 4.034A pdb=" N PHE 8 265 " --> pdb=" O SER 8 261 " (cutoff:3.500A) Processing helix chain '8' and resid 279 through 288 Processing helix chain '8' and resid 297 through 305 Processing helix chain '8' and resid 311 through 326 removed outlier: 3.500A pdb=" N ALA 8 317 " --> pdb=" O GLY 8 313 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR 8 326 " --> pdb=" O THR 8 322 " (cutoff:3.500A) Processing helix chain '8' and resid 329 through 342 removed outlier: 3.531A pdb=" N GLN 8 333 " --> pdb=" O PRO 8 329 " (cutoff:3.500A) Processing helix chain '8' and resid 347 through 363 Processing helix chain '8' and resid 371 through 379 Processing helix chain '8' and resid 397 through 401 Processing helix chain '8' and resid 429 through 432 No H-bonds generated for 'chain '8' and resid 429 through 432' Processing helix chain '8' and resid 437 through 446 Processing helix chain '8' and resid 458 through 467 Processing helix chain '8' and resid 470 through 472 No H-bonds generated for 'chain '8' and resid 470 through 472' Processing helix chain '8' and resid 478 through 489 Processing helix chain 'I' and resid 49 through 64 Processing helix chain 'I' and resid 86 through 92 removed outlier: 3.885A pdb=" N ILE I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 97 No H-bonds generated for 'chain 'I' and resid 95 through 97' Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 123 through 132 removed outlier: 4.051A pdb=" N GLN I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 186 No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 190 through 202 Proline residue: I 199 - end of helix Processing helix chain 'I' and resid 220 through 238 removed outlier: 4.020A pdb=" N VAL I 237 " --> pdb=" O LYS I 233 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE I 238 " --> pdb=" O ALA I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 249 removed outlier: 4.380A pdb=" N SER I 244 " --> pdb=" O LEU I 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 28 removed outlier: 3.612A pdb=" N VAL J 27 " --> pdb=" O ASN J 23 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR J 28 " --> pdb=" O VAL J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 69 Processing helix chain 'J' and resid 118 through 130 Processing helix chain 'J' and resid 182 through 191 removed outlier: 3.760A pdb=" N GLU J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 199 removed outlier: 4.595A pdb=" N HIS J 199 " --> pdb=" O ASP J 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 116 Processing helix chain 'K' and resid 135 through 139 Processing helix chain 'K' and resid 141 through 157 Processing helix chain 'K' and resid 176 through 184 Processing helix chain 'K' and resid 189 through 192 No H-bonds generated for 'chain 'K' and resid 189 through 192' Processing helix chain 'c' and resid 3 through 19 Processing helix chain 'c' and resid 23 through 36 removed outlier: 4.236A pdb=" N UNK c 28 " --> pdb=" O UNK c 24 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N UNK c 29 " --> pdb=" O UNK c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 58 Processing helix chain 'c' and resid 77 through 92 Processing helix chain 'c' and resid 106 through 123 Processing helix chain 'L' and resid 31 through 36 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 142 through 145 Processing sheet with id= A, first strand: chain '0' and resid 367 through 371 removed outlier: 6.854A pdb=" N ILE 0 455 " --> pdb=" O ILE 0 370 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU 0 190 " --> pdb=" O ILE 0 164 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ASP 0 166 " --> pdb=" O LEU 0 190 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP 0 192 " --> pdb=" O ASP 0 166 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N GLY 0 168 " --> pdb=" O ASP 0 192 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL 0 194 " --> pdb=" O GLY 0 168 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 402 through 407 Processing sheet with id= C, first strand: chain '0' and resid 502 through 504 Processing sheet with id= D, first strand: chain 'C' and resid 124 through 126 Processing sheet with id= E, first strand: chain 'C' and resid 141 through 144 Processing sheet with id= F, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.806A pdb=" N ASN C 396 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP C 327 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS C 394 " --> pdb=" O TRP C 327 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 3 through 5 Processing sheet with id= H, first strand: chain 'P' and resid 6 through 15 removed outlier: 3.581A pdb=" N ARG P 15 " --> pdb=" O SER P 18 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL P 25 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL P 39 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP P 64 " --> pdb=" O VAL P 44 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'Q' and resid 72 through 74 removed outlier: 14.117A pdb=" N ASN Q 5 " --> pdb=" O LYS Q 27 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N LYS Q 27 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU Q 7 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU Q 25 " --> pdb=" O LEU Q 7 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS Q 21 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Q' and resid 57 through 59 removed outlier: 6.658A pdb=" N ARG Q 59 " --> pdb=" O ILE Q 77 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE Q 77 " --> pdb=" O ARG Q 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 33 through 35 Processing sheet with id= L, first strand: chain 'W' and resid 93 through 95 Processing sheet with id= M, first strand: chain 'W' and resid 387 through 390 removed outlier: 6.455A pdb=" N THR W 341 " --> pdb=" O PHE W 146 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE W 148 " --> pdb=" O THR W 341 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU W 343 " --> pdb=" O ILE W 148 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'W' and resid 191 through 193 removed outlier: 3.653A pdb=" N LEU W 198 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'W' and resid 230 through 233 Processing sheet with id= P, first strand: chain 'Y' and resid 182 through 186 Processing sheet with id= Q, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.615A pdb=" N HIS A 294 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 283 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A 292 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 251 " --> pdb=" O MET A 293 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ALA A 295 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP A 253 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 297 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 255 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 244 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A 233 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA A 246 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE A 231 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 64 through 67 removed outlier: 6.819A pdb=" N THR A 76 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 269 through 271 removed outlier: 6.461A pdb=" N LEU B 319 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU B 249 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL B 321 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 357 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 346 " --> pdb=" O TYR B 357 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE B 359 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 210 through 214 removed outlier: 6.646A pdb=" N ILE B 219 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU B 213 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '3' and resid 163 through 169 removed outlier: 6.038A pdb=" N GLU 3 157 " --> pdb=" O PRO 3 220 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 130 through 132 Processing sheet with id= W, first strand: chain '4' and resid 195 through 202 removed outlier: 4.140A pdb=" N LYS 4 195 " --> pdb=" O ARG 4 174 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA 4 173 " --> pdb=" O PRO 4 269 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG 4 175 " --> pdb=" O TYR 4 267 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N TYR 4 267 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 179 through 186 removed outlier: 6.126A pdb=" N VAL E 171 " --> pdb=" O PRO E 148 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY E 173 " --> pdb=" O MET E 146 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N MET E 146 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 219 through 224 Processing sheet with id= Z, first strand: chain 'F' and resid 96 through 99 removed outlier: 4.194A pdb=" N LEU F 2 " --> pdb=" O VAL F 99 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 54 through 56 Processing sheet with id= AB, first strand: chain 'F' and resid 38 through 41 removed outlier: 6.374A pdb=" N LEU F 70 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '6' and resid 294 through 296 Processing sheet with id= AD, first strand: chain '6' and resid 334 through 336 Processing sheet with id= AE, first strand: chain 'G' and resid 164 through 167 Processing sheet with id= AF, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.799A pdb=" N SER H 47 " --> pdb=" O GLY H 76 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 89 through 91 removed outlier: 6.657A pdb=" N LEU H 128 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG H 153 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU H 126 " --> pdb=" O ARG H 153 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '8' and resid 39 through 44 removed outlier: 6.638A pdb=" N LEU 8 84 " --> pdb=" O ARG 8 48 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE 8 50 " --> pdb=" O LEU 8 84 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE 8 86 " --> pdb=" O ILE 8 50 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU 8 52 " --> pdb=" O ILE 8 86 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS 8 88 " --> pdb=" O LEU 8 52 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU 8 87 " --> pdb=" O PRO 8 137 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL 8 139 " --> pdb=" O LEU 8 87 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N SER 8 89 " --> pdb=" O VAL 8 139 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N PHE 8 141 " --> pdb=" O SER 8 89 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE 8 159 " --> pdb=" O THR 8 140 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N MET 8 142 " --> pdb=" O PHE 8 159 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE 8 161 " --> pdb=" O MET 8 142 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '8' and resid 167 through 169 removed outlier: 7.790A pdb=" N MET 8 147 " --> pdb=" O PHE 8 96 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA 8 98 " --> pdb=" O MET 8 147 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 154 through 160 Processing sheet with id= AK, first strand: chain 'J' and resid 136 through 142 removed outlier: 6.678A pdb=" N ALA J 113 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP J 44 " --> pdb=" O ILE J 111 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE J 111 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN J 46 " --> pdb=" O ARG J 109 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG J 109 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG J 48 " --> pdb=" O HIS J 107 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS J 107 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS J 108 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 82 through 88 Processing sheet with id= AM, first strand: chain 'K' and resid 120 through 127 removed outlier: 6.674A pdb=" N PHE K 91 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER K 125 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU K 89 " --> pdb=" O SER K 125 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER K 127 " --> pdb=" O THR K 87 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR K 87 " --> pdb=" O SER K 127 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS K 75 " --> pdb=" O VAL K 94 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU K 96 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL K 73 " --> pdb=" O GLU K 96 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL K 167 " --> pdb=" O VAL K 196 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE K 198 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N MET K 169 " --> pdb=" O ILE K 198 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP K 200 " --> pdb=" O MET K 169 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'L' and resid 123 through 125 removed outlier: 6.716A pdb=" N ARG L 82 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL L 65 " --> pdb=" O ALA L 80 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA L 80 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL L 67 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARG L 78 " --> pdb=" O VAL L 67 " (cutoff:3.500A) 2208 hydrogen bonds defined for protein. 6174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1070 hydrogen bonds 1842 hydrogen bond angles 0 basepair planarities 481 basepair parallelities 785 stacking parallelities Total time for adding SS restraints: 60.94 Time building geometry restraints manager: 36.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 43095 1.43 - 1.65: 48373 1.65 - 1.87: 363 1.87 - 2.09: 0 2.09 - 2.32: 12 Bond restraints: 91843 Sorted by residual: bond pdb=" C PRO J 78 " pdb=" N LEU J 79 " ideal model delta sigma weight residual 1.327 1.288 0.039 1.71e-02 3.42e+03 5.20e+00 bond pdb=" CG1 ILE 0 320 " pdb=" CD1 ILE 0 320 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.65e+00 bond pdb=" S1 SF4 0 701 " pdb="FE2 SF4 0 701 " ideal model delta sigma weight residual 2.280 2.221 0.059 3.00e-02 1.11e+03 3.87e+00 bond pdb=" S2 SF4 0 701 " pdb="FE1 SF4 0 701 " ideal model delta sigma weight residual 2.280 2.223 0.057 3.00e-02 1.11e+03 3.55e+00 bond pdb=" CB THR A 38 " pdb=" CG2 THR A 38 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.47e+00 ... (remaining 91838 not shown) Histogram of bond angle deviations from ideal: 71.59 - 85.20: 12 85.20 - 98.81: 5 98.81 - 112.42: 57411 112.42 - 126.04: 67915 126.04 - 139.65: 5856 Bond angle restraints: 131199 Sorted by residual: angle pdb=" C4' U a1464 " pdb=" C3' U a1464 " pdb=" O3' U a1464 " ideal model delta sigma weight residual 109.40 114.77 -5.37 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C GLN 8 44 " pdb=" N ASP 8 45 " pdb=" CA ASP 8 45 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" O3' G a 684 " pdb=" C3' G a 684 " pdb=" C2' G a 684 " ideal model delta sigma weight residual 109.50 114.50 -5.00 1.50e+00 4.44e-01 1.11e+01 angle pdb=" O3' G a 971 " pdb=" C3' G a 971 " pdb=" C2' G a 971 " ideal model delta sigma weight residual 113.70 118.68 -4.98 1.50e+00 4.44e-01 1.10e+01 angle pdb=" C1' U a 183 " pdb=" N1 U a 183 " pdb=" C2 U a 183 " ideal model delta sigma weight residual 117.70 127.41 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 131194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 52846 35.90 - 71.80: 3338 71.80 - 107.70: 274 107.70 - 143.60: 19 143.60 - 179.50: 26 Dihedral angle restraints: 56503 sinusoidal: 36508 harmonic: 19995 Sorted by residual: dihedral pdb=" O4' U a1130 " pdb=" C1' U a1130 " pdb=" N1 U a1130 " pdb=" C2 U a1130 " ideal model delta sinusoidal sigma weight residual -160.00 15.68 -175.68 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U a1448 " pdb=" C1' U a1448 " pdb=" N1 U a1448 " pdb=" C2 U a1448 " ideal model delta sinusoidal sigma weight residual -160.00 -4.19 -155.81 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U a1416 " pdb=" C1' U a1416 " pdb=" N1 U a1416 " pdb=" C2 U a1416 " ideal model delta sinusoidal sigma weight residual -160.00 -7.93 -152.07 1 1.50e+01 4.44e-03 8.04e+01 ... (remaining 56500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.204: 15842 4.204 - 8.409: 0 8.409 - 12.613: 0 12.613 - 16.818: 0 16.818 - 21.022: 4 Chirality restraints: 15846 Sorted by residual: chirality pdb="FE4 SF4 0 701 " pdb=" S1 SF4 0 701 " pdb=" S2 SF4 0 701 " pdb=" S3 SF4 0 701 " both_signs ideal model delta sigma weight residual False 10.55 -10.47 21.02 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 0 701 " pdb=" S2 SF4 0 701 " pdb=" S3 SF4 0 701 " pdb=" S4 SF4 0 701 " both_signs ideal model delta sigma weight residual False -10.55 10.43 -20.99 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE3 SF4 0 701 " pdb=" S1 SF4 0 701 " pdb=" S2 SF4 0 701 " pdb=" S4 SF4 0 701 " both_signs ideal model delta sigma weight residual False -10.55 10.33 -20.88 2.00e-01 2.50e+01 1.09e+04 ... (remaining 15843 not shown) Planarity restraints: 11150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU 4 309 " -0.084 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO 4 310 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO 4 310 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO 4 310 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A a1023 " 0.047 2.00e-02 2.50e+03 2.04e-02 1.14e+01 pdb=" N9 A a1023 " -0.044 2.00e-02 2.50e+03 pdb=" C8 A a1023 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A a1023 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A a1023 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A a1023 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A a1023 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A a1023 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A a1023 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A a1023 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A a1023 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 78 " -0.273 9.50e-02 1.11e+02 1.23e-01 1.02e+01 pdb=" NE ARG O 78 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG O 78 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG O 78 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG O 78 " -0.004 2.00e-02 2.50e+03 ... (remaining 11147 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 447 2.51 - 3.11: 62105 3.11 - 3.71: 155602 3.71 - 4.30: 228697 4.30 - 4.90: 329970 Nonbonded interactions: 776821 Sorted by model distance: nonbonded pdb=" OP2 A a 312 " pdb="MG MG a1753 " model vdw 1.914 2.170 nonbonded pdb=" OP2 A a 784 " pdb="MG MG a1731 " model vdw 1.925 2.170 nonbonded pdb="MG MG W 502 " pdb=" O HOH W 602 " model vdw 1.927 2.170 nonbonded pdb=" OP1 C a 356 " pdb="MG MG a1718 " model vdw 1.933 2.170 nonbonded pdb=" OP1 G a1597 " pdb="MG MG a1746 " model vdw 1.937 2.170 ... (remaining 776816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 16.510 Check model and map are aligned: 0.950 Set scattering table: 0.600 Process input model: 246.490 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.290 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: 0.030 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 282.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 0.084 91843 Z= 0.278 Angle : 0.669 9.708 131199 Z= 0.354 Chirality : 0.335 21.022 15846 Planarity : 0.006 0.127 11150 Dihedral : 19.369 179.496 43522 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 6594 helix: 0.92 (0.09), residues: 3048 sheet: -0.16 (0.20), residues: 634 loop : -0.09 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP 8 423 HIS 0.013 0.001 HIS 0 507 PHE 0.023 0.002 PHE 8 114 TYR 0.029 0.002 TYR W 179 ARG 0.017 0.001 ARG O 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1111 time to evaluate : 5.693 Fit side-chains revert: symmetry clash REVERT: 0 96 HIS cc_start: 0.5983 (m-70) cc_final: 0.5740 (m90) REVERT: C 180 MET cc_start: 0.7815 (mmt) cc_final: 0.7451 (mmt) REVERT: M 47 MET cc_start: 0.8381 (mmt) cc_final: 0.8150 (mmt) REVERT: S 62 ILE cc_start: 0.8483 (pt) cc_final: 0.8187 (pp) REVERT: U 70 ASN cc_start: 0.7847 (p0) cc_final: 0.7268 (p0) REVERT: V 217 LEU cc_start: 0.7374 (tt) cc_final: 0.7057 (tt) REVERT: W 245 PHE cc_start: 0.7493 (m-80) cc_final: 0.7005 (m-10) REVERT: 2 94 TYR cc_start: 0.5713 (t80) cc_final: 0.4842 (t80) REVERT: E 142 ARG cc_start: 0.7447 (mtm110) cc_final: 0.6663 (mtm110) REVERT: 8 240 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6985 (mt-10) REVERT: I 228 MET cc_start: 0.8786 (ttp) cc_final: 0.8459 (ttm) outliers start: 0 outliers final: 1 residues processed: 1111 average time/residue: 1.8671 time to fit residues: 2705.7217 Evaluate side-chains 805 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 804 time to evaluate : 5.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 691 optimal weight: 10.0000 chunk 620 optimal weight: 10.0000 chunk 344 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 418 optimal weight: 0.2980 chunk 331 optimal weight: 0.0670 chunk 641 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 390 optimal weight: 5.9990 chunk 477 optimal weight: 0.0470 chunk 743 optimal weight: 10.0000 overall best weight: 2.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 70 GLN 0 89 ASN 0 119 HIS 0 139 ASN 0 276 HIS ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 391 HIS 0 491 GLN ** 0 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 59 ASN C 91 ASN C 142 ASN C 297 ASN C 301 ASN O 48 GLN Q 218 ASN R 133 GLN S 54 HIS T 121 ASN T 154 HIS U 66 GLN U 71 ASN U 208 HIS V 60 HIS V 67 ASN V 89 ASN W 106 HIS W 201 GLN W 312 GLN W 449 HIS X 21 GLN X 58 HIS Y 148 HIS Y 243 HIS Y 246 GLN Y 297 HIS B 293 GLN B 298 ASN B 391 ASN 2 92 HIS 2 101 HIS 3 9 HIS 3 199 GLN D 407 GLN D 409 ASN D 449 HIS 4 38 GLN 4 222 GLN E 198 HIS F 61 HIS F 112 HIS ** 6 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 83 HIS 6 170 GLN 6 337 ASN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 224 HIS 8 259 ASN 8 283 ASN 8 302 ASN I 51 HIS I 122 ASN J 199 HIS L 57 GLN L 89 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.256 91843 Z= 0.258 Angle : 0.769 50.815 131199 Z= 0.451 Chirality : 0.106 6.334 15846 Planarity : 0.005 0.088 11150 Dihedral : 20.409 179.899 29425 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.03 % Allowed : 9.22 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.10), residues: 6594 helix: 1.27 (0.09), residues: 3044 sheet: 0.03 (0.20), residues: 637 loop : 0.09 (0.11), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 98 HIS 0.006 0.001 HIS T 154 PHE 0.018 0.002 PHE 0 402 TYR 0.021 0.002 TYR C 98 ARG 0.008 0.001 ARG S 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 845 time to evaluate : 5.661 Fit side-chains revert: symmetry clash REVERT: 0 320 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8157 (mp) REVERT: C 45 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.5820 (mpp) REVERT: C 180 MET cc_start: 0.7783 (mmt) cc_final: 0.7359 (mmt) REVERT: M 47 MET cc_start: 0.8390 (mmt) cc_final: 0.8057 (mmt) REVERT: P 116 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7596 (ttm-80) REVERT: S 35 THR cc_start: 0.8773 (p) cc_final: 0.8505 (t) REVERT: S 58 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6874 (pt0) REVERT: S 62 ILE cc_start: 0.8493 (pt) cc_final: 0.8255 (pp) REVERT: T 122 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6109 (ttp80) REVERT: U 70 ASN cc_start: 0.7848 (p0) cc_final: 0.7613 (p0) REVERT: U 152 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7981 (tpt-90) REVERT: W 245 PHE cc_start: 0.7494 (m-80) cc_final: 0.6877 (m-10) REVERT: Y 68 LEU cc_start: 0.8639 (mt) cc_final: 0.8416 (mt) REVERT: Y 105 LYS cc_start: 0.6267 (mtpp) cc_final: 0.6050 (mttm) REVERT: A 224 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.5774 (ptm-80) REVERT: 2 94 TYR cc_start: 0.5815 (t80) cc_final: 0.4954 (t80) REVERT: 4 60 GLN cc_start: 0.5348 (OUTLIER) cc_final: 0.4858 (mp10) REVERT: E 138 ASP cc_start: 0.6555 (t70) cc_final: 0.6225 (t70) REVERT: I 225 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: J 147 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6827 (mm-30) REVERT: K 93 SER cc_start: 0.7959 (p) cc_final: 0.7605 (p) outliers start: 122 outliers final: 55 residues processed: 903 average time/residue: 1.7350 time to fit residues: 2081.2696 Evaluate side-chains 839 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 774 time to evaluate : 5.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 320 ILE Chi-restraints excluded: chain 0 residue 396 ASP Chi-restraints excluded: chain 0 residue 464 ASN Chi-restraints excluded: chain 5 residue 72 GLN Chi-restraints excluded: chain 5 residue 211 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 116 ARG Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain S residue 58 GLU Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 203 VAL Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Z residue 54 LEU Chi-restraints excluded: chain Z residue 60 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain 3 residue 124 LYS Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain 4 residue 60 GLN Chi-restraints excluded: chain 4 residue 61 GLN Chi-restraints excluded: chain 4 residue 258 LYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain 6 residue 263 GLU Chi-restraints excluded: chain 6 residue 275 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain 8 residue 46 THR Chi-restraints excluded: chain 8 residue 292 SER Chi-restraints excluded: chain 8 residue 367 SER Chi-restraints excluded: chain 8 residue 393 GLU Chi-restraints excluded: chain 8 residue 448 THR Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 125 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 413 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 619 optimal weight: 6.9990 chunk 506 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 745 optimal weight: 10.0000 chunk 804 optimal weight: 30.0000 chunk 663 optimal weight: 20.0000 chunk 738 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 597 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 113 GLN ** 0 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN C 186 ASN C 254 HIS M 49 GLN O 48 GLN Q 218 ASN R 133 GLN U 187 GLN U 211 GLN V 73 ASN V 192 HIS ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 53 HIS Y 217 HIS Y 252 HIS B 293 GLN B 391 ASN 3 65 HIS 3 199 GLN 3 229 HIS D 409 ASN 4 135 ASN E 37 GLN ** 6 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 337 ASN G 151 GLN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN 8 283 ASN 8 302 ASN ** 8 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN J 122 GLN J 199 HIS L 51 GLN L 89 ASN L 124 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 91843 Z= 0.411 Angle : 0.849 50.573 131199 Z= 0.485 Chirality : 0.111 6.486 15846 Planarity : 0.006 0.061 11150 Dihedral : 20.434 179.900 29423 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.49 % Favored : 97.50 % Rotamer: Outliers : 3.23 % Allowed : 10.74 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.61 (0.10), residues: 6594 helix: 0.98 (0.09), residues: 3047 sheet: 0.08 (0.20), residues: 649 loop : 0.01 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 98 HIS 0.009 0.002 HIS W 106 PHE 0.022 0.002 PHE W 183 TYR 0.030 0.002 TYR C 98 ARG 0.008 0.001 ARG O 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 808 time to evaluate : 6.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 320 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8207 (mp) REVERT: C 45 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6513 (mpp) REVERT: C 180 MET cc_start: 0.7938 (mmt) cc_final: 0.7586 (mmt) REVERT: M 23 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7728 (mmmt) REVERT: M 47 MET cc_start: 0.8344 (mmt) cc_final: 0.8044 (mmt) REVERT: Q 105 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6722 (tmmm) REVERT: S 62 ILE cc_start: 0.8652 (pt) cc_final: 0.8386 (pp) REVERT: T 122 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6275 (ttp80) REVERT: U 152 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8059 (tpt-90) REVERT: U 183 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: Y 79 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: A 224 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.5817 (ptm-80) REVERT: B 390 ARG cc_start: 0.7105 (ptt-90) cc_final: 0.6855 (ptt-90) REVERT: D 384 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6164 (p0) REVERT: 4 121 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6978 (p0) REVERT: E 138 ASP cc_start: 0.6777 (t70) cc_final: 0.6446 (t70) REVERT: F 59 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5121 (pt0) REVERT: 6 273 ASN cc_start: 0.7535 (m-40) cc_final: 0.7162 (m-40) REVERT: 8 112 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6905 (mptt) REVERT: 8 232 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7219 (m-30) REVERT: 8 354 ASP cc_start: 0.7318 (m-30) cc_final: 0.6911 (m-30) REVERT: 8 384 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.5184 (mtm110) REVERT: J 147 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6861 (mm-30) outliers start: 194 outliers final: 100 residues processed: 928 average time/residue: 1.7655 time to fit residues: 2175.5480 Evaluate side-chains 891 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 776 time to evaluate : 5.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 320 ILE Chi-restraints excluded: chain 0 residue 396 ASP Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 464 ASN Chi-restraints excluded: chain 5 residue 72 GLN Chi-restraints excluded: chain 5 residue 211 LEU Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 112 LYS Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 115 GLU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain S residue 23 ILE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 183 GLU Chi-restraints excluded: chain U residue 203 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 411 VAL Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain W residue 445 LEU Chi-restraints excluded: chain W residue 446 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 183 THR Chi-restraints excluded: chain Y residue 193 GLU Chi-restraints excluded: chain Y residue 240 LYS Chi-restraints excluded: chain Y residue 293 GLU Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 60 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 3 residue 124 LYS Chi-restraints excluded: chain 3 residue 203 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain 4 residue 61 GLN Chi-restraints excluded: chain 4 residue 121 ASP Chi-restraints excluded: chain 4 residue 215 VAL Chi-restraints excluded: chain 4 residue 228 LYS Chi-restraints excluded: chain 4 residue 258 LYS Chi-restraints excluded: chain 4 residue 307 SER Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain 6 residue 263 GLU Chi-restraints excluded: chain 6 residue 275 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 241 ARG Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain 8 residue 46 THR Chi-restraints excluded: chain 8 residue 112 LYS Chi-restraints excluded: chain 8 residue 232 ASP Chi-restraints excluded: chain 8 residue 292 SER Chi-restraints excluded: chain 8 residue 367 SER Chi-restraints excluded: chain 8 residue 384 ARG Chi-restraints excluded: chain 8 residue 393 GLU Chi-restraints excluded: chain 8 residue 401 THR Chi-restraints excluded: chain 8 residue 448 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 186 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 736 optimal weight: 10.0000 chunk 560 optimal weight: 6.9990 chunk 386 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 chunk 500 optimal weight: 0.9990 chunk 747 optimal weight: 10.0000 chunk 791 optimal weight: 9.9990 chunk 390 optimal weight: 2.9990 chunk 708 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN O 48 GLN O 151 ASN Q 218 ASN U 211 GLN V 73 ASN ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 53 HIS ** Z 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 386 ASN B 391 ASN D 409 ASN ** 6 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 337 ASN G 151 GLN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 283 ASN ** 8 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN J 122 GLN L 89 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 91843 Z= 0.406 Angle : 0.842 50.555 131199 Z= 0.483 Chirality : 0.110 6.477 15846 Planarity : 0.005 0.059 11150 Dihedral : 20.416 179.590 29423 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.91 % Allowed : 11.49 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.50 (0.10), residues: 6594 helix: 0.86 (0.09), residues: 3053 sheet: 0.11 (0.20), residues: 631 loop : -0.04 (0.11), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 98 HIS 0.008 0.002 HIS L 124 PHE 0.025 0.002 PHE D 204 TYR 0.029 0.002 TYR C 98 ARG 0.007 0.001 ARG Y 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 785 time to evaluate : 5.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 204 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6749 (mtp85) REVERT: 0 320 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8230 (mp) REVERT: 5 271 LEU cc_start: 0.3046 (tm) cc_final: 0.2844 (tt) REVERT: 5 302 ARG cc_start: 0.3590 (OUTLIER) cc_final: 0.3371 (ptt180) REVERT: C 45 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6641 (mpp) REVERT: C 107 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7852 (tpt) REVERT: C 180 MET cc_start: 0.7906 (mmt) cc_final: 0.7474 (mmt) REVERT: M 23 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7732 (mmmt) REVERT: M 47 MET cc_start: 0.8321 (mmt) cc_final: 0.8018 (mmt) REVERT: O 148 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: P 116 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7603 (ttm-80) REVERT: Q 105 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6793 (tmmm) REVERT: T 122 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6341 (ttp80) REVERT: T 126 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: U 152 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8092 (tpt-90) REVERT: V 73 ASN cc_start: 0.7529 (t0) cc_final: 0.7256 (t0) REVERT: V 83 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.6026 (pt0) REVERT: W 210 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8189 (ttt90) REVERT: W 306 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: Y 53 HIS cc_start: 0.7008 (m-70) cc_final: 0.6610 (m170) REVERT: Y 68 LEU cc_start: 0.8729 (mt) cc_final: 0.8522 (mt) REVERT: Y 79 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: Y 207 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7881 (mttm) REVERT: 2 125 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7321 (ttmm) REVERT: D 3 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6726 (mtp85) REVERT: D 384 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6219 (p0) REVERT: 4 121 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6965 (p0) REVERT: 6 273 ASN cc_start: 0.7627 (m-40) cc_final: 0.7211 (m-40) REVERT: G 113 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8454 (t) REVERT: H 122 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: 8 112 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6784 (mptt) REVERT: 8 232 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7124 (m-30) REVERT: 8 257 MET cc_start: 0.8690 (mtp) cc_final: 0.8254 (mtm) REVERT: 8 354 ASP cc_start: 0.7339 (m-30) cc_final: 0.6910 (m-30) REVERT: 8 384 ARG cc_start: 0.5710 (OUTLIER) cc_final: 0.5183 (mtm110) REVERT: 8 412 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6249 (mtp) REVERT: I 128 GLU cc_start: 0.7196 (tp30) cc_final: 0.6705 (tp30) REVERT: I 225 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: I 254 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8690 (tmt170) REVERT: J 147 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6896 (mm-30) outliers start: 235 outliers final: 117 residues processed: 929 average time/residue: 1.8454 time to fit residues: 2287.2843 Evaluate side-chains 909 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 763 time to evaluate : 6.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 124 THR Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 194 VAL Chi-restraints excluded: chain 0 residue 204 ARG Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 320 ILE Chi-restraints excluded: chain 0 residue 396 ASP Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 464 ASN Chi-restraints excluded: chain 5 residue 72 GLN Chi-restraints excluded: chain 5 residue 211 LEU Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 302 ARG Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 48 MET Chi-restraints excluded: chain N residue 112 LYS Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 148 GLU Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 116 ARG Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain Q residue 220 LYS Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain S residue 23 ILE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain T residue 126 GLU Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 203 VAL Chi-restraints excluded: chain U residue 224 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 306 ARG Chi-restraints excluded: chain W residue 379 GLU Chi-restraints excluded: chain W residue 387 THR Chi-restraints excluded: chain W residue 411 VAL Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain W residue 445 LEU Chi-restraints excluded: chain W residue 446 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain Y residue 66 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 193 GLU Chi-restraints excluded: chain Y residue 207 LYS Chi-restraints excluded: chain Y residue 240 LYS Chi-restraints excluded: chain Y residue 293 GLU Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 60 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 125 LYS Chi-restraints excluded: chain 3 residue 124 LYS Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 121 ASP Chi-restraints excluded: chain 4 residue 215 VAL Chi-restraints excluded: chain 4 residue 228 LYS Chi-restraints excluded: chain 4 residue 258 LYS Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain 6 residue 263 GLU Chi-restraints excluded: chain 6 residue 275 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 241 ARG Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain 8 residue 46 THR Chi-restraints excluded: chain 8 residue 112 LYS Chi-restraints excluded: chain 8 residue 232 ASP Chi-restraints excluded: chain 8 residue 292 SER Chi-restraints excluded: chain 8 residue 367 SER Chi-restraints excluded: chain 8 residue 384 ARG Chi-restraints excluded: chain 8 residue 393 GLU Chi-restraints excluded: chain 8 residue 412 MET Chi-restraints excluded: chain 8 residue 448 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 82 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 659 optimal weight: 20.0000 chunk 449 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 589 optimal weight: 0.0010 chunk 326 optimal weight: 6.9990 chunk 675 optimal weight: 7.9990 chunk 547 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 404 optimal weight: 6.9990 chunk 710 optimal weight: 20.0000 chunk 199 optimal weight: 0.9980 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 113 GLN ** 0 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 141 HIS ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN O 48 GLN U 211 GLN ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 391 ASN 2 68 GLN 3 145 ASN D 409 ASN ** 6 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 337 ASN G 151 GLN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 283 ASN 8 420 ASN I 122 ASN J 122 GLN L 57 GLN L 89 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 91843 Z= 0.313 Angle : 0.788 50.451 131199 Z= 0.459 Chirality : 0.109 6.423 15846 Planarity : 0.005 0.065 11150 Dihedral : 20.321 179.636 29423 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.60 % Allowed : 12.57 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.10), residues: 6594 helix: 1.05 (0.09), residues: 3052 sheet: 0.13 (0.20), residues: 636 loop : 0.05 (0.11), residues: 2906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 98 HIS 0.005 0.001 HIS W 372 PHE 0.021 0.002 PHE E 238 TYR 0.025 0.002 TYR C 98 ARG 0.008 0.001 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 786 time to evaluate : 5.773 Fit side-chains revert: symmetry clash REVERT: 0 189 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: 0 204 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6668 (mtp85) REVERT: 5 194 HIS cc_start: 0.5132 (m170) cc_final: 0.4906 (m170) REVERT: 5 271 LEU cc_start: 0.3289 (tm) cc_final: 0.3065 (tt) REVERT: 5 302 ARG cc_start: 0.3586 (OUTLIER) cc_final: 0.3374 (ptt180) REVERT: C 45 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6658 (mpp) REVERT: C 107 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7874 (tpt) REVERT: M 23 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7720 (mmmt) REVERT: M 47 MET cc_start: 0.8321 (mmt) cc_final: 0.8005 (mmt) REVERT: M 61 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6452 (tm-30) REVERT: Q 105 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6796 (tmmm) REVERT: T 122 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6323 (ttp80) REVERT: U 152 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8055 (tpt-90) REVERT: V 73 ASN cc_start: 0.7474 (t0) cc_final: 0.7230 (t0) REVERT: W 182 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7726 (mp) REVERT: W 210 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8078 (ttt90) REVERT: W 306 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7858 (mtp85) REVERT: Y 79 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6041 (mp0) REVERT: Y 207 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7784 (mttm) REVERT: A 224 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.6357 (ptt180) REVERT: B 321 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8358 (t) REVERT: 2 125 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7247 (ttmm) REVERT: D 3 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6713 (mtp85) REVERT: D 384 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6191 (p0) REVERT: 4 24 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5630 (mt-10) REVERT: 6 273 ASN cc_start: 0.7556 (m-40) cc_final: 0.7184 (m-40) REVERT: G 113 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8439 (t) REVERT: H 13 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8973 (mp) REVERT: H 98 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7971 (mtt-85) REVERT: H 122 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: 8 232 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: 8 354 ASP cc_start: 0.7310 (m-30) cc_final: 0.6878 (m-30) REVERT: 8 384 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.5229 (mtm110) REVERT: 8 412 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6293 (mtp) REVERT: I 225 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: J 147 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6890 (mm-30) outliers start: 216 outliers final: 108 residues processed: 919 average time/residue: 1.8307 time to fit residues: 2239.8505 Evaluate side-chains 892 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 755 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 204 ARG Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 306 ILE Chi-restraints excluded: chain 0 residue 396 ASP Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 464 ASN Chi-restraints excluded: chain 5 residue 211 LEU Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 302 ARG Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain N residue 96 TYR Chi-restraints excluded: chain N residue 112 LYS Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 203 VAL Chi-restraints excluded: chain U residue 224 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 306 ARG Chi-restraints excluded: chain W residue 379 GLU Chi-restraints excluded: chain W residue 387 THR Chi-restraints excluded: chain W residue 411 VAL Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain W residue 445 LEU Chi-restraints excluded: chain W residue 446 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain Y residue 66 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 183 THR Chi-restraints excluded: chain Y residue 193 GLU Chi-restraints excluded: chain Y residue 207 LYS Chi-restraints excluded: chain Y residue 240 LYS Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 60 SER Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 125 LYS Chi-restraints excluded: chain 3 residue 124 LYS Chi-restraints excluded: chain 3 residue 203 LEU Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain 4 residue 24 GLU Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 87 LEU Chi-restraints excluded: chain 4 residue 258 LYS Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain 6 residue 263 GLU Chi-restraints excluded: chain 6 residue 275 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 241 ARG Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain 8 residue 46 THR Chi-restraints excluded: chain 8 residue 232 ASP Chi-restraints excluded: chain 8 residue 292 SER Chi-restraints excluded: chain 8 residue 367 SER Chi-restraints excluded: chain 8 residue 384 ARG Chi-restraints excluded: chain 8 residue 393 GLU Chi-restraints excluded: chain 8 residue 410 LEU Chi-restraints excluded: chain 8 residue 412 MET Chi-restraints excluded: chain 8 residue 446 LYS Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 478 ILE Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 75 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 266 optimal weight: 5.9990 chunk 712 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 464 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 792 optimal weight: 20.0000 chunk 657 optimal weight: 10.0000 chunk 366 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 262 optimal weight: 8.9990 chunk 416 optimal weight: 5.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 70 GLN ** 0 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 113 GLN ** 0 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 507 HIS ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN O 48 GLN U 211 GLN ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 28 ASN ** Z 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN 2 68 GLN D 409 ASN 4 229 GLN E 38 GLN ** 6 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 170 GLN 6 337 ASN G 116 HIS ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 283 ASN I 122 ASN I 131 GLN J 122 GLN L 57 GLN L 89 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 91843 Z= 0.431 Angle : 0.857 50.583 131199 Z= 0.489 Chirality : 0.111 6.481 15846 Planarity : 0.006 0.060 11150 Dihedral : 20.364 179.962 29423 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.96 % Allowed : 13.05 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.50 (0.10), residues: 6594 helix: 0.85 (0.09), residues: 3060 sheet: 0.12 (0.20), residues: 631 loop : -0.04 (0.11), residues: 2903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 98 HIS 0.008 0.002 HIS Q 39 PHE 0.021 0.002 PHE 5 150 TYR 0.031 0.003 TYR C 98 ARG 0.009 0.001 ARG T 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 773 time to evaluate : 5.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6760 (tpp) REVERT: M 23 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7697 (mmmm) REVERT: M 47 MET cc_start: 0.8323 (mmt) cc_final: 0.8020 (mmt) REVERT: Q 105 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6823 (tmmm) REVERT: T 122 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6306 (ttp80) REVERT: T 124 MET cc_start: 0.7994 (mmp) cc_final: 0.7740 (mmm) REVERT: T 175 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8148 (mptt) REVERT: U 152 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8098 (tpt-90) REVERT: V 73 ASN cc_start: 0.7467 (t0) cc_final: 0.7235 (t0) REVERT: V 83 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.5971 (pt0) REVERT: W 210 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8197 (ttt90) REVERT: W 306 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7904 (mtp85) REVERT: Y 79 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6142 (mp0) REVERT: Y 207 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7902 (mttm) REVERT: A 224 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6447 (ptt180) REVERT: 2 125 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7315 (ttmm) REVERT: D 3 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6726 (mtp85) REVERT: D 384 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6222 (p0) REVERT: 4 121 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6979 (p0) REVERT: E 20 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7733 (tp) REVERT: 6 170 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6951 (mt0) REVERT: 6 200 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7756 (mtp180) REVERT: 6 273 ASN cc_start: 0.7610 (m-40) cc_final: 0.7257 (m-40) REVERT: 6 301 GLU cc_start: 0.6291 (pp20) cc_final: 0.6077 (pp20) REVERT: 6 338 LYS cc_start: 0.7079 (ttmm) cc_final: 0.6864 (tptm) REVERT: G 113 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8426 (t) REVERT: H 13 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8935 (mp) REVERT: H 98 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8023 (mpt-90) REVERT: 8 232 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: 8 354 ASP cc_start: 0.7342 (m-30) cc_final: 0.6899 (m-30) REVERT: 8 384 ARG cc_start: 0.5686 (OUTLIER) cc_final: 0.5154 (mtm110) REVERT: 8 412 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6432 (mtp) REVERT: 8 439 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: I 225 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: I 254 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8681 (tmt170) REVERT: J 147 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6880 (mm-30) outliers start: 238 outliers final: 128 residues processed: 929 average time/residue: 1.8623 time to fit residues: 2286.4035 Evaluate side-chains 900 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 745 time to evaluate : 5.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 396 ASP Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 464 ASN Chi-restraints excluded: chain 0 residue 466 LEU Chi-restraints excluded: chain 5 residue 211 LEU Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 112 LYS Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 116 ARG Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain Q residue 220 LYS Chi-restraints excluded: chain S residue 23 ILE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain T residue 175 LYS Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 203 VAL Chi-restraints excluded: chain U residue 224 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 306 ARG Chi-restraints excluded: chain W residue 387 THR Chi-restraints excluded: chain W residue 411 VAL Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain W residue 445 LEU Chi-restraints excluded: chain W residue 446 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 61 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain Y residue 64 ARG Chi-restraints excluded: chain Y residue 66 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 183 THR Chi-restraints excluded: chain Y residue 193 GLU Chi-restraints excluded: chain Y residue 207 LYS Chi-restraints excluded: chain Y residue 240 LYS Chi-restraints excluded: chain Y residue 293 GLU Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 60 SER Chi-restraints excluded: chain Z residue 92 LYS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 87 ILE Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 125 LYS Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 124 LYS Chi-restraints excluded: chain 3 residue 203 LEU Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 87 LEU Chi-restraints excluded: chain 4 residue 121 ASP Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain 4 residue 215 VAL Chi-restraints excluded: chain 4 residue 258 LYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain 6 residue 170 GLN Chi-restraints excluded: chain 6 residue 263 GLU Chi-restraints excluded: chain 6 residue 275 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 241 ARG Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain 8 residue 46 THR Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 212 THR Chi-restraints excluded: chain 8 residue 232 ASP Chi-restraints excluded: chain 8 residue 292 SER Chi-restraints excluded: chain 8 residue 367 SER Chi-restraints excluded: chain 8 residue 384 ARG Chi-restraints excluded: chain 8 residue 393 GLU Chi-restraints excluded: chain 8 residue 410 LEU Chi-restraints excluded: chain 8 residue 412 MET Chi-restraints excluded: chain 8 residue 439 GLU Chi-restraints excluded: chain 8 residue 446 LYS Chi-restraints excluded: chain 8 residue 448 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 478 ILE Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 82 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 763 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 451 optimal weight: 0.8980 chunk 578 optimal weight: 8.9990 chunk 448 optimal weight: 10.0000 chunk 667 optimal weight: 40.0000 chunk 442 optimal weight: 8.9990 chunk 789 optimal weight: 0.2980 chunk 494 optimal weight: 1.9990 chunk 481 optimal weight: 5.9990 chunk 364 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 113 GLN ** 0 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN O 48 GLN U 68 HIS U 211 GLN ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 28 ASN ** Z 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN 2 68 GLN D 409 ASN 6 46 HIS 6 337 ASN G 151 GLN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 283 ASN I 122 ASN I 131 GLN J 122 GLN L 57 GLN L 89 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 91843 Z= 0.230 Angle : 0.743 50.465 131199 Z= 0.439 Chirality : 0.107 6.352 15846 Planarity : 0.004 0.049 11150 Dihedral : 20.221 179.749 29423 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.91 % Allowed : 14.63 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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 (0.10), residues: 6594 helix: 1.27 (0.09), residues: 3056 sheet: 0.25 (0.20), residues: 633 loop : 0.12 (0.12), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G 98 HIS 0.006 0.001 HIS 5 194 PHE 0.029 0.001 PHE 6 225 TYR 0.035 0.001 TYR K 76 ARG 0.016 0.000 ARG 0 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 781 time to evaluate : 5.755 Fit side-chains revert: symmetry clash REVERT: 5 302 ARG cc_start: 0.3490 (OUTLIER) cc_final: 0.3274 (ptt180) REVERT: C 45 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6472 (mtt) REVERT: C 186 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7369 (t0) REVERT: M 47 MET cc_start: 0.8317 (mmt) cc_final: 0.8001 (mmt) REVERT: O 110 ARG cc_start: 0.6581 (mmm-85) cc_final: 0.6305 (mtp-110) REVERT: R 64 ARG cc_start: 0.8026 (tpt-90) cc_final: 0.7741 (tpt170) REVERT: R 104 THR cc_start: 0.8142 (m) cc_final: 0.7892 (p) REVERT: T 99 ARG cc_start: 0.4300 (tmm160) cc_final: 0.3886 (tmt170) REVERT: T 122 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6258 (ttp80) REVERT: U 152 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8027 (tpt-90) REVERT: W 210 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8108 (ttt90) REVERT: W 306 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.6398 (mtp180) REVERT: Y 79 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: A 224 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6318 (ptt180) REVERT: D 384 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6200 (p0) REVERT: 4 24 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.5577 (mt-10) REVERT: 4 121 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6923 (p0) REVERT: 6 273 ASN cc_start: 0.7638 (m-40) cc_final: 0.7234 (m-40) REVERT: G 113 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8420 (t) REVERT: H 98 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7750 (mtt-85) REVERT: 8 232 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: 8 354 ASP cc_start: 0.7311 (m-30) cc_final: 0.6911 (m-30) REVERT: 8 384 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5228 (mtm110) REVERT: 8 391 LYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6238 (mttt) REVERT: 8 412 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6178 (mtp) REVERT: I 36 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7639 (mtm180) REVERT: I 225 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: I 254 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8703 (tmt170) outliers start: 175 outliers final: 84 residues processed: 897 average time/residue: 1.8638 time to fit residues: 2244.2183 Evaluate side-chains 856 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 751 time to evaluate : 5.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 124 THR Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 306 ILE Chi-restraints excluded: chain 0 residue 396 ASP Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 466 LEU Chi-restraints excluded: chain 5 residue 211 LEU Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain 5 residue 302 ARG Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 96 TYR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 178 LYS Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 306 ARG Chi-restraints excluded: chain W residue 387 THR Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain W residue 446 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 64 ARG Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 183 THR Chi-restraints excluded: chain Y residue 193 GLU Chi-restraints excluded: chain Y residue 240 LYS Chi-restraints excluded: chain Z residue 54 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 58 THR Chi-restraints excluded: chain 2 residue 87 ILE Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 203 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain 4 residue 24 GLU Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 87 LEU Chi-restraints excluded: chain 4 residue 121 ASP Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain 6 residue 263 GLU Chi-restraints excluded: chain 6 residue 275 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 241 ARG Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain 8 residue 46 THR Chi-restraints excluded: chain 8 residue 232 ASP Chi-restraints excluded: chain 8 residue 292 SER Chi-restraints excluded: chain 8 residue 367 SER Chi-restraints excluded: chain 8 residue 384 ARG Chi-restraints excluded: chain 8 residue 391 LYS Chi-restraints excluded: chain 8 residue 410 LEU Chi-restraints excluded: chain 8 residue 412 MET Chi-restraints excluded: chain 8 residue 446 LYS Chi-restraints excluded: chain 8 residue 478 ILE Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 75 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 488 optimal weight: 3.9990 chunk 315 optimal weight: 0.0000 chunk 471 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 501 optimal weight: 9.9990 chunk 537 optimal weight: 4.9990 chunk 390 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 620 optimal weight: 10.0000 overall best weight: 2.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 113 GLN ** 0 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN O 48 GLN ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 53 HIS Z 28 ASN ** Z 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 391 ASN 2 68 GLN D 409 ASN 6 337 ASN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 109 ASN 8 283 ASN I 122 ASN J 122 GLN L 57 GLN L 89 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.243 91843 Z= 0.275 Angle : 0.761 50.449 131199 Z= 0.446 Chirality : 0.108 6.393 15846 Planarity : 0.004 0.073 11150 Dihedral : 20.153 179.531 29423 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.78 % Allowed : 15.18 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.95 (0.10), residues: 6594 helix: 1.28 (0.09), residues: 3048 sheet: 0.26 (0.20), residues: 637 loop : 0.14 (0.12), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 98 HIS 0.006 0.001 HIS 5 194 PHE 0.028 0.002 PHE 6 225 TYR 0.041 0.002 TYR K 76 ARG 0.008 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 760 time to evaluate : 5.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 518 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: C 45 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6501 (mtt) REVERT: C 186 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7411 (t0) REVERT: M 47 MET cc_start: 0.8329 (mmt) cc_final: 0.8002 (mmt) REVERT: O 110 ARG cc_start: 0.6566 (mmm-85) cc_final: 0.6319 (mtp-110) REVERT: P 116 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7579 (ttm-80) REVERT: R 64 ARG cc_start: 0.8066 (tpt-90) cc_final: 0.7793 (tpt170) REVERT: T 122 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6185 (ttp80) REVERT: T 124 MET cc_start: 0.7832 (mmp) cc_final: 0.7630 (mmm) REVERT: U 152 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8026 (tpt-90) REVERT: V 132 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6590 (tp) REVERT: W 182 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7752 (mp) REVERT: W 210 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8080 (ttt90) REVERT: W 306 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.6432 (mtp180) REVERT: Y 53 HIS cc_start: 0.6970 (m-70) cc_final: 0.6547 (m170) REVERT: Y 79 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6151 (mp0) REVERT: Y 207 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7746 (mttm) REVERT: 2 125 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7244 (ttmm) REVERT: D 384 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6225 (p0) REVERT: 4 24 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.5576 (mt-10) REVERT: 4 121 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6898 (p0) REVERT: 6 273 ASN cc_start: 0.7649 (m-40) cc_final: 0.7248 (m-40) REVERT: G 113 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8428 (t) REVERT: H 98 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7804 (mtt-85) REVERT: 8 232 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: 8 354 ASP cc_start: 0.7316 (m-30) cc_final: 0.6895 (m-30) REVERT: 8 384 ARG cc_start: 0.5783 (OUTLIER) cc_final: 0.5274 (mtm110) REVERT: 8 412 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6190 (mtp) REVERT: I 36 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8196 (ttm110) REVERT: I 225 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: I 254 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8699 (tmt170) outliers start: 167 outliers final: 101 residues processed: 867 average time/residue: 1.8054 time to fit residues: 2081.9188 Evaluate side-chains 878 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 753 time to evaluate : 5.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 124 THR Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 194 VAL Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 306 ILE Chi-restraints excluded: chain 0 residue 396 ASP Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 464 ASN Chi-restraints excluded: chain 0 residue 466 LEU Chi-restraints excluded: chain 0 residue 518 GLU Chi-restraints excluded: chain 5 residue 211 LEU Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 96 TYR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 116 ARG Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 178 LYS Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 140 LEU Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 306 ARG Chi-restraints excluded: chain W residue 387 THR Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain W residue 446 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 64 ARG Chi-restraints excluded: chain Y residue 66 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 183 THR Chi-restraints excluded: chain Y residue 193 GLU Chi-restraints excluded: chain Y residue 207 LYS Chi-restraints excluded: chain Y residue 240 LYS Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 54 LEU Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 58 THR Chi-restraints excluded: chain 2 residue 125 LYS Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 203 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain 4 residue 24 GLU Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 121 ASP Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain 6 residue 263 GLU Chi-restraints excluded: chain 6 residue 275 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 241 ARG Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain 8 residue 46 THR Chi-restraints excluded: chain 8 residue 232 ASP Chi-restraints excluded: chain 8 residue 245 PHE Chi-restraints excluded: chain 8 residue 292 SER Chi-restraints excluded: chain 8 residue 367 SER Chi-restraints excluded: chain 8 residue 384 ARG Chi-restraints excluded: chain 8 residue 410 LEU Chi-restraints excluded: chain 8 residue 412 MET Chi-restraints excluded: chain 8 residue 446 LYS Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 198 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 82 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 718 optimal weight: 10.0000 chunk 756 optimal weight: 20.0000 chunk 689 optimal weight: 8.9990 chunk 735 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 chunk 577 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 664 optimal weight: 10.0000 chunk 695 optimal weight: 10.0000 chunk 733 optimal weight: 10.0000 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 113 GLN ** 0 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 194 HIS ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN O 48 GLN S 71 HIS U 211 GLN V 73 ASN ** V 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 28 ASN ** Z 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 300 ASN B 391 ASN 2 68 GLN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 ASN E 38 GLN 6 170 GLN 6 337 ASN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 283 ASN I 122 ASN J 122 GLN L 57 GLN L 89 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 91843 Z= 0.477 Angle : 0.880 50.609 131199 Z= 0.498 Chirality : 0.112 6.494 15846 Planarity : 0.006 0.076 11150 Dihedral : 20.303 178.762 29423 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.98 % Allowed : 15.30 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.54 (0.10), residues: 6594 helix: 0.86 (0.09), residues: 3065 sheet: 0.18 (0.20), residues: 629 loop : -0.01 (0.11), residues: 2900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP G 98 HIS 0.009 0.002 HIS Q 39 PHE 0.031 0.003 PHE 6 225 TYR 0.047 0.003 TYR K 76 ARG 0.016 0.001 ARG 0 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 753 time to evaluate : 5.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 195 ARG cc_start: 0.3313 (OUTLIER) cc_final: 0.2554 (ttt-90) REVERT: M 47 MET cc_start: 0.8334 (mmt) cc_final: 0.7982 (mmt) REVERT: O 110 ARG cc_start: 0.6608 (mmm-85) cc_final: 0.6370 (mtp-110) REVERT: P 116 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7778 (ttm-80) REVERT: Q 105 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6858 (tmmm) REVERT: R 64 ARG cc_start: 0.8118 (tpt-90) cc_final: 0.7814 (tpt170) REVERT: T 122 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6240 (ttp80) REVERT: U 152 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8082 (tpt-90) REVERT: V 83 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5857 (pt0) REVERT: V 132 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6648 (tp) REVERT: W 182 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7851 (mp) REVERT: W 210 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8223 (ttt90) REVERT: W 306 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7944 (mtp85) REVERT: Y 79 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: Y 207 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7867 (mttm) REVERT: 2 125 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7266 (ttmm) REVERT: D 3 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6724 (mtp180) REVERT: D 384 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6198 (p0) REVERT: 4 121 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6943 (p0) REVERT: 6 170 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6908 (mt0) REVERT: 6 273 ASN cc_start: 0.7673 (m-40) cc_final: 0.7274 (m-40) REVERT: G 113 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8426 (t) REVERT: H 98 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7979 (mpt-90) REVERT: H 153 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.7592 (mtp85) REVERT: 8 232 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: 8 354 ASP cc_start: 0.7350 (m-30) cc_final: 0.6900 (m-30) REVERT: 8 384 ARG cc_start: 0.5680 (OUTLIER) cc_final: 0.5147 (mtm110) REVERT: 8 412 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6369 (mtp) REVERT: I 36 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7748 (mtm180) REVERT: I 225 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: I 254 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8681 (tmt170) REVERT: K 154 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7949 (mt) outliers start: 179 outliers final: 106 residues processed: 876 average time/residue: 1.8044 time to fit residues: 2102.2678 Evaluate side-chains 870 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 737 time to evaluate : 5.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 124 THR Chi-restraints excluded: chain 0 residue 181 ILE Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 194 VAL Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 396 ASP Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 464 ASN Chi-restraints excluded: chain 5 residue 194 HIS Chi-restraints excluded: chain 5 residue 195 ARG Chi-restraints excluded: chain 5 residue 211 LEU Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 116 ARG Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 178 LYS Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain S residue 23 ILE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 306 ARG Chi-restraints excluded: chain W residue 387 THR Chi-restraints excluded: chain W residue 411 VAL Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain W residue 446 VAL Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 64 ARG Chi-restraints excluded: chain Y residue 66 LEU Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 183 THR Chi-restraints excluded: chain Y residue 193 GLU Chi-restraints excluded: chain Y residue 207 LYS Chi-restraints excluded: chain Y residue 240 LYS Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 58 THR Chi-restraints excluded: chain 2 residue 125 LYS Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 203 LEU Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 87 LEU Chi-restraints excluded: chain 4 residue 121 ASP Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain 4 residue 215 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain 6 residue 170 GLN Chi-restraints excluded: chain 6 residue 263 GLU Chi-restraints excluded: chain 6 residue 275 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 241 ARG Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain 8 residue 46 THR Chi-restraints excluded: chain 8 residue 232 ASP Chi-restraints excluded: chain 8 residue 292 SER Chi-restraints excluded: chain 8 residue 367 SER Chi-restraints excluded: chain 8 residue 384 ARG Chi-restraints excluded: chain 8 residue 410 LEU Chi-restraints excluded: chain 8 residue 412 MET Chi-restraints excluded: chain 8 residue 446 LYS Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 82 ARG Chi-restraints excluded: chain L residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 483 optimal weight: 5.9990 chunk 777 optimal weight: 4.9990 chunk 474 optimal weight: 5.9990 chunk 369 optimal weight: 6.9990 chunk 540 optimal weight: 0.8980 chunk 815 optimal weight: 0.7980 chunk 750 optimal weight: 6.9990 chunk 649 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 501 optimal weight: 0.7980 chunk 398 optimal weight: 0.9980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 113 GLN ** 0 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN O 48 GLN U 211 GLN ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 188 ASN Z 28 ASN ** Z 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 391 ASN D 139 HIS ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 ASN 6 337 ASN G 151 GLN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 283 ASN I 122 ASN J 122 GLN K 109 ASN L 57 GLN L 89 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 91843 Z= 0.239 Angle : 0.755 50.480 131199 Z= 0.443 Chirality : 0.107 6.364 15846 Planarity : 0.004 0.072 11150 Dihedral : 20.173 179.985 29423 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.36 % Allowed : 16.25 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 6594 helix: 1.23 (0.09), residues: 3059 sheet: 0.33 (0.20), residues: 630 loop : 0.12 (0.12), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 98 HIS 0.023 0.001 HIS 5 194 PHE 0.030 0.001 PHE 6 225 TYR 0.046 0.001 TYR K 76 ARG 0.011 0.000 ARG F 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13188 Ramachandran restraints generated. 6594 Oldfield, 0 Emsley, 6594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 758 time to evaluate : 5.761 Fit side-chains revert: symmetry clash REVERT: 0 462 ASP cc_start: 0.3089 (t0) cc_final: 0.2874 (t0) REVERT: C 186 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7331 (t0) REVERT: M 47 MET cc_start: 0.8312 (mmt) cc_final: 0.7991 (mmt) REVERT: Q 105 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6865 (tmmm) REVERT: R 64 ARG cc_start: 0.8030 (tpt-90) cc_final: 0.7762 (tpt170) REVERT: T 122 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6153 (ttp80) REVERT: U 152 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8026 (tpt-90) REVERT: V 31 ASP cc_start: 0.6682 (p0) cc_final: 0.6444 (p0) REVERT: V 132 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6607 (tp) REVERT: W 210 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8075 (ttt90) REVERT: W 306 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7845 (mtp85) REVERT: Y 53 HIS cc_start: 0.6924 (m-70) cc_final: 0.6465 (m170) REVERT: 2 125 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7292 (ttmm) REVERT: D 384 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6189 (p0) REVERT: 4 121 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6902 (p0) REVERT: 6 273 ASN cc_start: 0.7559 (m-40) cc_final: 0.7199 (m-40) REVERT: G 113 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8422 (t) REVERT: H 98 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7747 (mtt-85) REVERT: H 125 GLU cc_start: 0.7842 (tt0) cc_final: 0.7517 (tt0) REVERT: H 153 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7690 (mtp85) REVERT: 8 232 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: 8 354 ASP cc_start: 0.7288 (m-30) cc_final: 0.6892 (m-30) REVERT: 8 384 ARG cc_start: 0.5759 (OUTLIER) cc_final: 0.5213 (mtm110) REVERT: 8 412 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6261 (mtp) REVERT: 8 439 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6482 (tt0) REVERT: I 225 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: I 254 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8704 (tmt170) REVERT: L 82 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7545 (mmt180) outliers start: 142 outliers final: 89 residues processed: 856 average time/residue: 1.7832 time to fit residues: 2027.5831 Evaluate side-chains 854 residues out of total 6015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 745 time to evaluate : 5.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 124 THR Chi-restraints excluded: chain 0 residue 194 VAL Chi-restraints excluded: chain 0 residue 290 ASP Chi-restraints excluded: chain 0 residue 306 ILE Chi-restraints excluded: chain 0 residue 396 ASP Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 5 residue 211 LEU Chi-restraints excluded: chain 5 residue 297 LEU Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 24 VAL Chi-restraints excluded: chain Q residue 52 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 89 GLU Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 178 LYS Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain T residue 122 ARG Chi-restraints excluded: chain U residue 98 THR Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 230 LEU Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 164 LEU Chi-restraints excluded: chain V residue 223 VAL Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 247 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 306 ARG Chi-restraints excluded: chain W residue 387 THR Chi-restraints excluded: chain W residue 417 ILE Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 64 ARG Chi-restraints excluded: chain Y residue 66 LEU Chi-restraints excluded: chain Y residue 68 LEU Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 183 THR Chi-restraints excluded: chain Y residue 193 GLU Chi-restraints excluded: chain Y residue 240 LYS Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain 2 residue 38 VAL Chi-restraints excluded: chain 2 residue 58 THR Chi-restraints excluded: chain 2 residue 125 LYS Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 203 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 87 LEU Chi-restraints excluded: chain 4 residue 121 ASP Chi-restraints excluded: chain 4 residue 133 THR Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain 6 residue 263 GLU Chi-restraints excluded: chain 6 residue 275 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 241 ARG Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain 8 residue 46 THR Chi-restraints excluded: chain 8 residue 232 ASP Chi-restraints excluded: chain 8 residue 292 SER Chi-restraints excluded: chain 8 residue 367 SER Chi-restraints excluded: chain 8 residue 384 ARG Chi-restraints excluded: chain 8 residue 393 GLU Chi-restraints excluded: chain 8 residue 410 LEU Chi-restraints excluded: chain 8 residue 412 MET Chi-restraints excluded: chain 8 residue 439 GLU Chi-restraints excluded: chain 8 residue 446 LYS Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 8 residue 478 ILE Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 82 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 819 random chunks: chunk 516 optimal weight: 7.9990 chunk 692 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 599 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 650 optimal weight: 10.0000 chunk 272 optimal weight: 0.9980 chunk 668 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 113 GLN ** 0 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN O 48 GLN Q 196 ASN U 211 GLN V 73 ASN Z 28 ASN ** Z 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN B 298 ASN ** D 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 ASN 4 229 GLN 6 337 ASN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 283 ASN ** 8 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN J 122 GLN K 109 ASN L 51 GLN L 57 GLN L 89 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.139942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105472 restraints weight = 101312.633| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.04 r_work: 0.2924 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 91843 Z= 0.252 Angle : 0.754 50.444 131199 Z= 0.443 Chirality : 0.107 6.378 15846 Planarity : 0.004 0.072 11150 Dihedral : 20.077 179.638 29423 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.23 % Allowed : 16.41 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 1.01 (0.10), residues: 6594 helix: 1.32 (0.09), residues: 3054 sheet: 0.38 (0.20), residues: 626 loop : 0.16 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 98 HIS 0.005 0.001 HIS T 154 PHE 0.029 0.002 PHE 6 225 TYR 0.044 0.002 TYR K 76 ARG 0.017 0.000 ARG 0 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31814.11 seconds wall clock time: 554 minutes 25.15 seconds (33265.15 seconds total)