Starting phenix.real_space_refine on Fri Mar 22 04:49:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pss_20462/03_2024/6pss_20462.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pss_20462/03_2024/6pss_20462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pss_20462/03_2024/6pss_20462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pss_20462/03_2024/6pss_20462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pss_20462/03_2024/6pss_20462.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pss_20462/03_2024/6pss_20462.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 86 5.49 5 Mg 1 5.21 5 S 140 5.16 5 C 20018 2.51 5 N 5722 2.21 5 O 6391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 7": "OE1" <-> "OE2" Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 118": "OD1" <-> "OD2" Residue "G ASP 120": "OD1" <-> "OD2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "H ASP 96": "OD1" <-> "OD2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H ASP 118": "OD1" <-> "OD2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H ASP 197": "OD1" <-> "OD2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "I GLU 7": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I ASP 320": "OD1" <-> "OD2" Residue "I GLU 334": "OE1" <-> "OE2" Residue "I GLU 349": "OE1" <-> "OE2" Residue "I ASP 358": "OD1" <-> "OD2" Residue "I GLU 365": "OE1" <-> "OE2" Residue "I TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I GLU 382": "OE1" <-> "OE2" Residue "I ASP 393": "OD1" <-> "OD2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 413": "OE1" <-> "OE2" Residue "I GLU 415": "OE1" <-> "OE2" Residue "I ASP 443": "OD1" <-> "OD2" Residue "I GLU 477": "OE1" <-> "OE2" Residue "I PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 549": "OD1" <-> "OD2" Residue "I GLU 610": "OE1" <-> "OE2" Residue "I GLU 625": "OE1" <-> "OE2" Residue "I GLU 626": "OE1" <-> "OE2" Residue "I GLU 631": "OE1" <-> "OE2" Residue "I TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 705": "OE1" <-> "OE2" Residue "I GLU 738": "OE1" <-> "OE2" Residue "I TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 745": "OE1" <-> "OE2" Residue "I TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 781": "OD1" <-> "OD2" Residue "I ASP 842": "OD1" <-> "OD2" Residue "I ASP 881": "OD1" <-> "OD2" Residue "I GLU 892": "OE1" <-> "OE2" Residue "I GLU 940": "OE1" <-> "OE2" Residue "I ASP 942": "OD1" <-> "OD2" Residue "I GLU 987": "OE1" <-> "OE2" Residue "I ASP 995": "OD1" <-> "OD2" Residue "I GLU 1006": "OE1" <-> "OE2" Residue "I GLU 1016": "OE1" <-> "OE2" Residue "I ASP 1019": "OD1" <-> "OD2" Residue "I TYR 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1150": "OD1" <-> "OD2" Residue "I ASP 1154": "OD1" <-> "OD2" Residue "I ASP 1160": "OD1" <-> "OD2" Residue "I ASP 1166": "OD1" <-> "OD2" Residue "I GLU 1174": "OE1" <-> "OE2" Residue "I ASP 1188": "OD1" <-> "OD2" Residue "I GLU 1197": "OE1" <-> "OE2" Residue "I TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1296": "OD1" <-> "OD2" Residue "I GLU 1329": "OE1" <-> "OE2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J GLU 175": "OE1" <-> "OE2" Residue "J GLU 195": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 207": "OE1" <-> "OE2" Residue "J ASP 256": "OD1" <-> "OD2" Residue "J ARG 259": "NH1" <-> "NH2" Residue "J ASP 267": "OD1" <-> "OD2" Residue "J ASP 289": "OD1" <-> "OD2" Residue "J ASP 304": "OD1" <-> "OD2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J GLU 443": "OE1" <-> "OE2" Residue "J TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 523": "OE1" <-> "OE2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 684": "OD1" <-> "OD2" Residue "J ASP 699": "OD1" <-> "OD2" Residue "J PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 738": "NH1" <-> "NH2" Residue "J TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J ASP 802": "OD1" <-> "OD2" Residue "J ASP 812": "OD1" <-> "OD2" Residue "J GLU 818": "OE1" <-> "OE2" Residue "J ASP 837": "OD1" <-> "OD2" Residue "J GLU 913": "OE1" <-> "OE2" Residue "J GLU 981": "OE1" <-> "OE2" Residue "J GLU 1009": "OE1" <-> "OE2" Residue "J GLU 1015": "OE1" <-> "OE2" Residue "J ASP 1042": "OD1" <-> "OD2" Residue "J ASP 1073": "OD1" <-> "OD2" Residue "J ASP 1082": "OD1" <-> "OD2" Residue "J ASP 1087": "OD1" <-> "OD2" Residue "J ASP 1094": "OD1" <-> "OD2" Residue "J PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1110": "OE1" <-> "OE2" Residue "J PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1187": "OE1" <-> "OE2" Residue "J GLU 1188": "OE1" <-> "OE2" Residue "J PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J ASP 1212": "OD1" <-> "OD2" Residue "J GLU 1215": "OE1" <-> "OE2" Residue "J TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1273": "OD1" <-> "OD2" Residue "J GLU 1281": "OE1" <-> "OE2" Residue "J GLU 1291": "OE1" <-> "OE2" Residue "J GLU 1327": "OE1" <-> "OE2" Residue "J GLU 1343": "OE1" <-> "OE2" Residue "J ASP 1368": "OD1" <-> "OD2" Residue "J ARG 1372": "NH1" <-> "NH2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K GLU 41": "OE1" <-> "OE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L ASP 63": "OD1" <-> "OD2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L GLU 88": "OE1" <-> "OE2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "L ASP 118": "OD1" <-> "OD2" Residue "L ASP 125": "OD1" <-> "OD2" Residue "L TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 160": "OD1" <-> "OD2" Residue "L GLU 215": "OE1" <-> "OE2" Residue "L ASP 267": "OD1" <-> "OD2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L GLU 310": "OE1" <-> "OE2" Residue "L GLU 335": "OE1" <-> "OE2" Residue "L GLU 336": "OE1" <-> "OE2" Residue "L TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 407": "OE1" <-> "OE2" Residue "L ARG 422": "NH1" <-> "NH2" Residue "L ARG 476": "NH1" <-> "NH2" Residue "L GLU 477": "OE1" <-> "OE2" Residue "L GLU 491": "OE1" <-> "OE2" Residue "L ASP 492": "OD1" <-> "OD2" Residue "L GLU 508": "OE1" <-> "OE2" Residue "L ASP 514": "OD1" <-> "OD2" Residue "L GLU 515": "OE1" <-> "OE2" Residue "L GLU 529": "OE1" <-> "OE2" Residue "L GLU 538": "OE1" <-> "OE2" Residue "L GLU 574": "OE1" <-> "OE2" Residue "L ARG 608": "NH1" <-> "NH2" Residue "M ASP 250": "OD1" <-> "OD2" Residue "M GLU 286": "OE1" <-> "OE2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "M ASP 305": "OD1" <-> "OD2" Residue "M GLU 319": "OE1" <-> "OE2" Residue "N GLU 13": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32361 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1769 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 10502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10502 Classifications: {'peptide': 1337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "J" Number of atoms: 10449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10449 Classifications: {'peptide': 1343} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1285} Chain breaks: 2 Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 4489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4489 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 5, 'PTRANS': 16, 'TRANS': 536} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 566 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 883 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "P" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 881 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14403 SG CYS J 72 52.032 63.342 117.405 1.00 49.80 S ATOM 14511 SG CYS J 85 49.490 64.794 119.548 1.00 56.66 S ATOM 14535 SG CYS J 88 51.826 67.255 118.243 1.00 62.07 S ATOM 20223 SG CYS J 814 22.847 115.222 82.104 1.00 37.86 S ATOM 20788 SG CYS J 888 26.266 114.307 82.777 1.00 25.54 S ATOM 20839 SG CYS J 895 24.770 112.696 79.240 1.00 26.49 S ATOM 20860 SG CYS J 898 25.820 116.471 79.796 1.00 23.63 S ATOM 30303 SG CYS N 37 73.399 155.719 76.959 1.00 55.81 S ATOM 30460 SG CYS N 58 77.917 154.245 75.816 1.00 53.67 S Time building chain proxies: 16.01, per 1000 atoms: 0.49 Number of scatterers: 32361 At special positions: 0 Unit cell: (146.9, 191.1, 191.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 140 16.00 P 86 15.00 Mg 1 11.99 O 6391 8.00 N 5722 7.00 C 20018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.48 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " Number of angles added : 6 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7260 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 51 sheets defined 41.8% alpha, 12.5% beta 39 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 11.59 Creating SS restraints... Processing helix chain 'G' and resid 35 through 50 Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.930A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.547A pdb=" N ILE G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 232 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.853A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 87 Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.692A pdb=" N LYS I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 207 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 272 through 280 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.559A pdb=" N LEU I 325 " --> pdb=" O LEU I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 352 Processing helix chain 'I' and resid 358 through 371 removed outlier: 3.612A pdb=" N VAL I 364 " --> pdb=" O LEU I 360 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU I 365 " --> pdb=" O SER I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 379 through 390 removed outlier: 3.534A pdb=" N LEU I 384 " --> pdb=" O ALA I 380 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN I 387 " --> pdb=" O SER I 383 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 removed outlier: 3.592A pdb=" N ILE I 426 " --> pdb=" O LYS I 422 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL I 428 " --> pdb=" O ASP I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 466 removed outlier: 3.789A pdb=" N GLU I 461 " --> pdb=" O GLY I 457 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN I 462 " --> pdb=" O GLU I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 471 Processing helix chain 'I' and resid 471 through 479 removed outlier: 3.530A pdb=" N VAL I 475 " --> pdb=" O VAL I 471 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU I 477 " --> pdb=" O ARG I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 506 removed outlier: 3.550A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU I 504 " --> pdb=" O ALA I 500 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.673A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.670A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 4.247A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 656 through 661 removed outlier: 4.228A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL I 661 " --> pdb=" O GLN I 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.856A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 removed outlier: 3.605A pdb=" N ASN I 684 " --> pdb=" O LEU I 680 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 737 through 741 removed outlier: 3.551A pdb=" N GLU I 740 " --> pdb=" O ASN I 737 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 737 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 860 through 865 removed outlier: 3.543A pdb=" N SER I 863 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 901 through 906 Processing helix chain 'I' and resid 942 through 975 removed outlier: 3.526A pdb=" N GLU I 949 " --> pdb=" O ALA I 945 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU I 960 " --> pdb=" O ALA I 956 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER I 973 " --> pdb=" O ALA I 969 " (cutoff:3.500A) Processing helix chain 'I' and resid 977 through 981 removed outlier: 4.018A pdb=" N VAL I 980 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 998 Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.284A pdb=" N GLU I1016 " --> pdb=" O GLU I1012 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE I1036 " --> pdb=" O LYS I1032 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR I1037 " --> pdb=" O ARG I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.774A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.323A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.685A pdb=" N LYS I1127 " --> pdb=" O GLY I1123 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA I1130 " --> pdb=" O ASP I1126 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1149 removed outlier: 3.647A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN I1146 " --> pdb=" O ARG I1142 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG I1147 " --> pdb=" O GLU I1143 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.575A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1175 removed outlier: 3.519A pdb=" N MET I1170 " --> pdb=" O ASP I1166 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.508A pdb=" N ILE I1195 " --> pdb=" O LYS I1191 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS I1196 " --> pdb=" O GLU I1192 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1280 Processing helix chain 'I' and resid 1283 through 1289 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.660A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN I1307 " --> pdb=" O LYS I1303 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1331 removed outlier: 3.582A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL I1325 " --> pdb=" O GLU I1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 122 through 129 removed outlier: 3.599A pdb=" N ASP J 129 " --> pdb=" O GLY J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.575A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 170 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 206 Processing helix chain 'J' and resid 211 through 231 removed outlier: 4.008A pdb=" N LEU J 223 " --> pdb=" O LYS J 219 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY J 231 " --> pdb=" O PHE J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 263 through 285 removed outlier: 4.090A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.533A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.516A pdb=" N PHE J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.780A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.924A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.775A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 613 through 634 removed outlier: 3.918A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.708A pdb=" N ASP J 643 " --> pdb=" O GLY J 640 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 640 through 644' Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 removed outlier: 3.638A pdb=" N SER J 728 " --> pdb=" O MET J 724 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.550A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 790 removed outlier: 3.738A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 791 through 793 No H-bonds generated for 'chain 'J' and resid 791 through 793' Processing helix chain 'J' and resid 794 through 804 removed outlier: 3.724A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.834A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.721A pdb=" N SER J 887 " --> pdb=" O SER J 884 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 900 removed outlier: 3.539A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 896 through 900' Processing helix chain 'J' and resid 914 through 928 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.822A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE J1145 " --> pdb=" O VAL J1141 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 removed outlier: 3.604A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1237 removed outlier: 3.725A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1237 through 1245 removed outlier: 3.697A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1261 removed outlier: 3.902A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1292 removed outlier: 3.856A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) Processing helix chain 'J' and resid 1321 through 1326 removed outlier: 3.868A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.790A pdb=" N ALA J1338 " --> pdb=" O GLU J1334 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1362 through 1372 removed outlier: 3.847A pdb=" N ARG J1372 " --> pdb=" O ASP J1368 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.819A pdb=" N LEU K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.934A pdb=" N GLU K 74 " --> pdb=" O GLN K 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 23 through 31 removed outlier: 3.667A pdb=" N VAL L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 50 removed outlier: 3.962A pdb=" N ILE L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU L 42 " --> pdb=" O SER L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 66 removed outlier: 4.142A pdb=" N LEU L 65 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 85 Processing helix chain 'L' and resid 96 through 107 removed outlier: 3.732A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 136 Processing helix chain 'L' and resid 137 through 151 removed outlier: 4.277A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 162 Processing helix chain 'L' and resid 213 through 233 removed outlier: 3.596A pdb=" N PHE L 221 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA L 226 " --> pdb=" O ALA L 222 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L 231 " --> pdb=" O GLN L 227 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP L 233 " --> pdb=" O VAL L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 255 removed outlier: 3.512A pdb=" N VAL L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 289 removed outlier: 4.830A pdb=" N LEU L 269 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL L 270 " --> pdb=" O PHE L 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG L 279 " --> pdb=" O VAL L 275 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL L 280 " --> pdb=" O MET L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 305 Processing helix chain 'L' and resid 324 through 329 removed outlier: 3.576A pdb=" N GLU L 328 " --> pdb=" O LYS L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 333 Processing helix chain 'L' and resid 336 through 349 removed outlier: 3.621A pdb=" N ALA L 340 " --> pdb=" O GLU L 336 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN L 345 " --> pdb=" O LEU L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 383 removed outlier: 3.686A pdb=" N ARG L 363 " --> pdb=" O LYS L 359 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG L 374 " --> pdb=" O ALA L 370 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 392 removed outlier: 3.593A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER L 389 " --> pdb=" O ARG L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 removed outlier: 3.567A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP L 417 " --> pdb=" O MET L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 446 removed outlier: 3.870A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR L 432 " --> pdb=" O SER L 428 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR L 440 " --> pdb=" O ARG L 436 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 468 removed outlier: 3.652A pdb=" N ARG L 468 " --> pdb=" O ASN L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 469 through 472 removed outlier: 3.623A pdb=" N GLN L 472 " --> pdb=" O GLN L 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 469 through 472' Processing helix chain 'L' and resid 479 through 487 removed outlier: 3.573A pdb=" N ALA L 484 " --> pdb=" O PRO L 480 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 500 removed outlier: 3.724A pdb=" N LEU L 498 " --> pdb=" O ILE L 494 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE L 500 " --> pdb=" O LYS L 496 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 522 removed outlier: 3.590A pdb=" N PHE L 522 " --> pdb=" O LEU L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 548 Processing helix chain 'L' and resid 549 through 551 No H-bonds generated for 'chain 'L' and resid 549 through 551' Processing helix chain 'L' and resid 552 through 562 removed outlier: 3.523A pdb=" N ALA L 556 " --> pdb=" O THR L 552 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS L 557 " --> pdb=" O ALA L 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 580 removed outlier: 3.604A pdb=" N PHE L 580 " --> pdb=" O VAL L 576 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 598 Processing helix chain 'L' and resid 606 through 611 Processing helix chain 'M' and resid 256 through 260 removed outlier: 3.917A pdb=" N LEU M 260 " --> pdb=" O VAL M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 273 Processing helix chain 'M' and resid 277 through 282 removed outlier: 3.672A pdb=" N LEU M 281 " --> pdb=" O TYR M 277 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL M 282 " --> pdb=" O ILE M 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 277 through 282' Processing helix chain 'M' and resid 285 through 291 Processing helix chain 'M' and resid 296 through 308 Processing helix chain 'N' and resid 6 through 25 Processing helix chain 'N' and resid 26 through 28 No H-bonds generated for 'chain 'N' and resid 26 through 28' Processing helix chain 'N' and resid 45 through 52 Processing helix chain 'N' and resid 58 through 70 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 18 removed outlier: 6.396A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 184 " --> pdb=" O GLU G 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.620A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 102 " --> pdb=" O MET G 142 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 110 Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 20 removed outlier: 3.532A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 53 through 60 removed outlier: 7.119A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'H' and resid 187 through 188 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.768A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.854A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU I 106 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL I 114 " --> pdb=" O GLU I 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.701A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.677A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL I 228 " --> pdb=" O THR I 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.442A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 580 through 581 removed outlier: 6.571A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.772A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 748 through 752 removed outlier: 5.746A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.655A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 835 through 841 removed outlier: 5.619A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD1, first strand: chain 'I' and resid 888 through 889 Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.588A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.514A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1338 through 1339 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 4.327A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 161 Processing sheet with id=AD7, first strand: chain 'J' and resid 252 through 254 Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 removed outlier: 7.372A pdb=" N LEU J 527 " --> pdb=" O ARG J 551 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N THR J 553 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 703 through 706 Processing sheet with id=AE1, first strand: chain 'J' and resid 745 through 748 removed outlier: 7.944A pdb=" N GLY J 745 " --> pdb=" O THR J 757 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR J 757 " --> pdb=" O GLY J 745 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET J 747 " --> pdb=" O ILE J 755 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 821 through 822 removed outlier: 3.640A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL J 843 " --> pdb=" O ARG J 883 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.935A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 935 through 936 Processing sheet with id=AE6, first strand: chain 'J' and resid 957 through 960 removed outlier: 6.531A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.214A pdb=" N VAL J 966 " --> pdb=" O VAL J 974 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL J 974 " --> pdb=" O VAL J 966 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'J' and resid 1002 through 1003 Processing sheet with id=AE9, first strand: chain 'J' and resid 1079 through 1081 removed outlier: 3.752A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE J1115 " --> pdb=" O GLY J1033 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1050 through 1051 removed outlier: 4.194A pdb=" N ASP J1051 " --> pdb=" O LEU J1056 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU J1056 " --> pdb=" O ASP J1051 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'J' and resid 1106 through 1107 Processing sheet with id=AF3, first strand: chain 'J' and resid 1156 through 1157 removed outlier: 4.037A pdb=" N ASP J1208 " --> pdb=" O ALA J1157 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF5, first strand: chain 'J' and resid 1172 through 1173 Processing sheet with id=AF6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.974A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL J1267 " --> pdb=" O THR J1301 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 14.93 Time building geometry restraints manager: 13.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7999 1.33 - 1.45: 6319 1.45 - 1.57: 18277 1.57 - 1.69: 172 1.69 - 1.82: 244 Bond restraints: 33011 Sorted by residual: bond pdb=" CA ARG I 687 " pdb=" C ARG I 687 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.41e-02 5.03e+03 1.56e+01 bond pdb=" C GLU J 418 " pdb=" N HIS J 419 " ideal model delta sigma weight residual 1.332 1.300 0.032 8.60e-03 1.35e+04 1.38e+01 bond pdb=" CA PHE I1270 " pdb=" CB PHE I1270 " ideal model delta sigma weight residual 1.526 1.464 0.062 1.76e-02 3.23e+03 1.25e+01 bond pdb=" C VAL I 550 " pdb=" N HIS I 551 " ideal model delta sigma weight residual 1.331 1.270 0.061 2.07e-02 2.33e+03 8.56e+00 bond pdb=" C LEU M 254 " pdb=" N ARG M 255 " ideal model delta sigma weight residual 1.331 1.392 -0.061 2.07e-02 2.33e+03 8.55e+00 ... (remaining 33006 not shown) Histogram of bond angle deviations from ideal: 96.82 - 105.17: 915 105.17 - 113.51: 18814 113.51 - 121.86: 18148 121.86 - 130.21: 6934 130.21 - 138.55: 138 Bond angle restraints: 44949 Sorted by residual: angle pdb=" C THR L 569 " pdb=" N ASP L 570 " pdb=" CA ASP L 570 " ideal model delta sigma weight residual 121.70 136.83 -15.13 1.80e+00 3.09e-01 7.07e+01 angle pdb=" C GLY I 544 " pdb=" N PHE I 545 " pdb=" CA PHE I 545 " ideal model delta sigma weight residual 121.70 135.39 -13.69 1.80e+00 3.09e-01 5.78e+01 angle pdb=" C ILE J 707 " pdb=" N ASN J 708 " pdb=" CA ASN J 708 " ideal model delta sigma weight residual 121.70 134.85 -13.15 1.80e+00 3.09e-01 5.34e+01 angle pdb=" C MET L 51 " pdb=" N GLY L 52 " pdb=" CA GLY L 52 " ideal model delta sigma weight residual 121.70 133.07 -11.37 1.80e+00 3.09e-01 3.99e+01 angle pdb=" C ILE L 511 " pdb=" N GLY L 512 " pdb=" CA GLY L 512 " ideal model delta sigma weight residual 121.70 132.37 -10.67 1.80e+00 3.09e-01 3.51e+01 ... (remaining 44944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 18828 35.59 - 71.18: 1262 71.18 - 106.77: 55 106.77 - 142.36: 1 142.36 - 177.95: 4 Dihedral angle restraints: 20150 sinusoidal: 8898 harmonic: 11252 Sorted by residual: dihedral pdb=" CA GLU L 503 " pdb=" C GLU L 503 " pdb=" N PRO L 504 " pdb=" CA PRO L 504 " ideal model delta harmonic sigma weight residual -180.00 -130.87 -49.13 0 5.00e+00 4.00e-02 9.65e+01 dihedral pdb=" CA VAL I 857 " pdb=" C VAL I 857 " pdb=" N GLY I 858 " pdb=" CA GLY I 858 " ideal model delta harmonic sigma weight residual -180.00 -143.38 -36.62 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA PRO N 33 " pdb=" C PRO N 33 " pdb=" N VAL N 34 " pdb=" CA VAL N 34 " ideal model delta harmonic sigma weight residual 180.00 -145.64 -34.36 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 20147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4476 0.084 - 0.168: 620 0.168 - 0.253: 50 0.253 - 0.337: 0 0.337 - 0.421: 1 Chirality restraints: 5147 Sorted by residual: chirality pdb=" CB VAL H 202 " pdb=" CA VAL H 202 " pdb=" CG1 VAL H 202 " pdb=" CG2 VAL H 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CB ILE I 524 " pdb=" CA ILE I 524 " pdb=" CG1 ILE I 524 " pdb=" CG2 ILE I 524 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN M 320 " pdb=" N ASN M 320 " pdb=" C ASN M 320 " pdb=" CB ASN M 320 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 5144 not shown) Planarity restraints: 5573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 854 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO I 855 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO I 855 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO I 855 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO I 190 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 120 " 0.051 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO J 121 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO J 121 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 121 " 0.043 5.00e-02 4.00e+02 ... (remaining 5570 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 27 2.31 - 2.96: 14140 2.96 - 3.61: 47691 3.61 - 4.25: 78474 4.25 - 4.90: 128085 Nonbonded interactions: 268417 Sorted by model distance: nonbonded pdb=" OD1 ASP L 149 " pdb=" NH2 ARG L 225 " model vdw 1.663 2.520 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.073 2.170 nonbonded pdb=" CG ASP L 149 " pdb=" NH2 ARG L 225 " model vdw 2.146 3.350 nonbonded pdb=" OH TYR J 360 " pdb=" OE1 GLN J 448 " model vdw 2.220 2.440 nonbonded pdb=" O ASN J 962 " pdb=" OG1 THR J 980 " model vdw 2.253 2.440 ... (remaining 268412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 158 or resid 171 through 233)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 228 or (resid 229 through 230 an \ d (name N or name CA or name C or name O or name CB )) or resid 231 through 233) \ ) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.020 Extract box with map and model: 5.630 Check model and map are aligned: 0.530 Set scattering table: 0.290 Process input model: 98.230 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.008 0.078 33011 Z= 0.548 Angle : 1.076 18.255 44949 Z= 0.613 Chirality : 0.057 0.421 5147 Planarity : 0.007 0.098 5573 Dihedral : 20.992 177.949 12890 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.66 % Favored : 92.13 % Rotamer: Outliers : 11.08 % Allowed : 22.55 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.16 % 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: -4.70 (0.10), residues: 3875 helix: -3.48 (0.08), residues: 1501 sheet: -2.60 (0.23), residues: 437 loop : -2.90 (0.12), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP J1020 HIS 0.012 0.002 HIS M 276 PHE 0.026 0.003 PHE J1325 TYR 0.039 0.003 TYR G 177 ARG 0.010 0.001 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 600 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 177 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: G 208 ASN cc_start: 0.7648 (p0) cc_final: 0.7219 (p0) REVERT: H 68 TYR cc_start: 0.3552 (OUTLIER) cc_final: 0.2760 (m-10) REVERT: H 233 ASP cc_start: 0.5699 (OUTLIER) cc_final: 0.5229 (p0) REVERT: I 29 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7476 (p) REVERT: I 90 VAL cc_start: 0.7719 (t) cc_final: 0.7453 (p) REVERT: I 202 ARG cc_start: 0.7009 (ptt90) cc_final: 0.6236 (ptp-110) REVERT: I 232 ILE cc_start: 0.5684 (OUTLIER) cc_final: 0.5039 (pt) REVERT: I 272 ARG cc_start: 0.6126 (mmp80) cc_final: 0.5854 (mmp80) REVERT: I 274 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.5304 (pt) REVERT: I 286 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.5198 (tm-30) REVERT: I 330 HIS cc_start: 0.0302 (OUTLIER) cc_final: -0.0326 (m-70) REVERT: I 386 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6634 (tp30) REVERT: I 496 LYS cc_start: 0.7225 (tptm) cc_final: 0.6753 (ttpp) REVERT: I 498 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7309 (mt) REVERT: I 620 ASN cc_start: 0.8170 (p0) cc_final: 0.7937 (p0) REVERT: I 641 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6223 (pp20) REVERT: I 706 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7699 (tpp-160) REVERT: I 894 GLN cc_start: 0.6205 (mt0) cc_final: 0.5731 (mt0) REVERT: I 941 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7010 (mptt) REVERT: I 974 ARG cc_start: 0.6364 (mtp180) cc_final: 0.5993 (ttp-170) REVERT: I 989 LEU cc_start: 0.5681 (tp) cc_final: 0.4567 (tp) REVERT: I 1085 MET cc_start: 0.8487 (mmm) cc_final: 0.7348 (mmm) REVERT: I 1117 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8660 (tp) REVERT: I 1129 ASN cc_start: 0.8155 (t0) cc_final: 0.7868 (t0) REVERT: I 1136 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6748 (mm-40) REVERT: I 1239 VAL cc_start: 0.8825 (p) cc_final: 0.8541 (p) REVERT: J 137 ARG cc_start: 0.6726 (mtm180) cc_final: 0.6214 (mtp85) REVERT: J 201 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5437 (tt) REVERT: J 203 GLU cc_start: 0.6039 (mt-10) cc_final: 0.5792 (mt-10) REVERT: J 235 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: J 479 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7868 (mt-10) REVERT: J 489 ASN cc_start: 0.7675 (m-40) cc_final: 0.7054 (p0) REVERT: J 560 ASN cc_start: 0.6200 (OUTLIER) cc_final: 0.5678 (m-40) REVERT: J 598 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6982 (tptm) REVERT: J 649 LYS cc_start: 0.7236 (mmtt) cc_final: 0.7020 (mmtp) REVERT: J 737 ILE cc_start: 0.8742 (mm) cc_final: 0.8462 (mm) REVERT: J 838 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6867 (ptp90) REVERT: J 871 LEU cc_start: 0.7237 (tp) cc_final: 0.6934 (tp) REVERT: J 1261 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8427 (pp) REVERT: K 52 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7189 (mtm110) REVERT: L 53 ILE cc_start: 0.4290 (OUTLIER) cc_final: 0.4067 (mp) REVERT: L 90 GLU cc_start: 0.1656 (OUTLIER) cc_final: 0.0892 (mm-30) REVERT: L 98 VAL cc_start: 0.5515 (OUTLIER) cc_final: 0.5188 (p) REVERT: L 99 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6310 (tpt170) REVERT: L 121 LYS cc_start: 0.7213 (ptpp) cc_final: 0.6508 (tppt) REVERT: L 129 GLN cc_start: 0.4558 (tt0) cc_final: 0.4310 (tt0) REVERT: L 476 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.3149 (mtm180) REVERT: L 477 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6872 (mt-10) REVERT: L 488 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.5263 (mt) REVERT: L 489 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5319 (mmt) REVERT: L 610 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.6153 (t80) outliers start: 368 outliers final: 208 residues processed: 915 average time/residue: 0.4773 time to fit residues: 670.7935 Evaluate side-chains 662 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 429 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1111 GLN Chi-restraints excluded: chain I residue 1117 LEU Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 85 CYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 337 ARG Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 598 LYS Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 838 ARG Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 861 ASN Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1050 THR Chi-restraints excluded: chain J residue 1058 SER Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1234 VAL Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 418 LYS Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 516 ASP Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 539 SER Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 599 ARG Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 3.9990 chunk 299 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 309 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS I 330 HIS I 343 HIS I 387 ASN I 437 ASN I 447 HIS ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 649 GLN I 658 GLN I 684 ASN I 799 ASN I 811 ASN I 955 GLN I1080 ASN I1116 HIS I1134 GLN I1157 GLN I1175 ASN J 153 ASN J 206 ASN J 266 ASN J 294 ASN ** J 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN J 519 ASN J 545 HIS J 680 ASN J 702 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 979 ASN J1010 GLN J1023 HIS ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1126 GLN J1227 HIS L 8 GLN L 28 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN L 472 GLN N 62 GLN N 68 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33011 Z= 0.216 Angle : 0.656 12.357 44949 Z= 0.348 Chirality : 0.043 0.204 5147 Planarity : 0.005 0.087 5573 Dihedral : 17.838 177.314 5629 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 8.16 % Allowed : 25.44 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.12), residues: 3875 helix: -1.81 (0.11), residues: 1559 sheet: -2.03 (0.26), residues: 378 loop : -2.52 (0.12), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 997 HIS 0.007 0.001 HIS L 600 PHE 0.017 0.001 PHE L 256 TYR 0.020 0.001 TYR I1229 ARG 0.006 0.000 ARG L 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 488 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 208 ASN cc_start: 0.7669 (p0) cc_final: 0.7252 (p0) REVERT: H 35 PHE cc_start: 0.8555 (m-80) cc_final: 0.8325 (m-80) REVERT: I 90 VAL cc_start: 0.7838 (t) cc_final: 0.7492 (p) REVERT: I 202 ARG cc_start: 0.6902 (ptt90) cc_final: 0.6370 (ptp-110) REVERT: I 274 ILE cc_start: 0.5772 (OUTLIER) cc_final: 0.5427 (pt) REVERT: I 330 HIS cc_start: 0.0787 (OUTLIER) cc_final: -0.0339 (m170) REVERT: I 371 ARG cc_start: 0.3977 (ttm110) cc_final: 0.3565 (ttm110) REVERT: I 386 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6621 (tp30) REVERT: I 453 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8272 (tt) REVERT: I 496 LYS cc_start: 0.7386 (tptm) cc_final: 0.6861 (ttpp) REVERT: I 498 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7369 (pt) REVERT: I 646 SER cc_start: 0.7763 (OUTLIER) cc_final: 0.7539 (t) REVERT: I 684 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7784 (m110) REVERT: I 791 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8238 (tt) REVERT: I 894 GLN cc_start: 0.6256 (mt0) cc_final: 0.5883 (mt0) REVERT: I 941 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7130 (mptt) REVERT: I 984 VAL cc_start: 0.3266 (OUTLIER) cc_final: 0.2842 (m) REVERT: I 989 LEU cc_start: 0.5601 (tp) cc_final: 0.4652 (tp) REVERT: I 1085 MET cc_start: 0.8431 (mmm) cc_final: 0.6638 (mmm) REVERT: I 1129 ASN cc_start: 0.8136 (t0) cc_final: 0.7869 (t0) REVERT: I 1188 ASP cc_start: 0.7642 (t0) cc_final: 0.7435 (t0) REVERT: I 1239 VAL cc_start: 0.8837 (p) cc_final: 0.8589 (p) REVERT: J 137 ARG cc_start: 0.6826 (mtm180) cc_final: 0.6266 (mtp85) REVERT: J 201 LEU cc_start: 0.6176 (mm) cc_final: 0.5610 (tp) REVERT: J 203 GLU cc_start: 0.6060 (mt-10) cc_final: 0.5681 (mt-10) REVERT: J 204 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.4958 (pm20) REVERT: J 402 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.4981 (tm-30) REVERT: J 489 ASN cc_start: 0.7377 (m-40) cc_final: 0.6697 (p0) REVERT: J 644 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7795 (mtm) REVERT: J 664 ILE cc_start: 0.7924 (mp) cc_final: 0.7705 (mp) REVERT: J 709 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.4952 (tpm-80) REVERT: J 866 GLU cc_start: 0.6645 (mp0) cc_final: 0.6394 (mp0) REVERT: J 1061 VAL cc_start: 0.0960 (OUTLIER) cc_final: 0.0204 (m) REVERT: J 1244 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7577 (mm-40) REVERT: J 1261 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8299 (pp) REVERT: K 18 ASP cc_start: 0.5725 (m-30) cc_final: 0.5498 (m-30) REVERT: K 53 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6652 (mt-10) REVERT: L 90 GLU cc_start: 0.1702 (OUTLIER) cc_final: 0.0754 (mm-30) REVERT: L 99 ARG cc_start: 0.6985 (mtt180) cc_final: 0.6349 (tpt170) REVERT: L 121 LYS cc_start: 0.7203 (ptpp) cc_final: 0.6405 (tppt) REVERT: L 277 MET cc_start: 0.4605 (tpt) cc_final: 0.4212 (mtt) REVERT: L 413 MET cc_start: 0.7195 (mtm) cc_final: 0.6797 (tmm) REVERT: L 418 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6285 (ttpt) REVERT: L 460 ILE cc_start: 0.8439 (mt) cc_final: 0.8227 (tp) REVERT: L 476 ARG cc_start: 0.4906 (OUTLIER) cc_final: 0.2970 (mtm180) REVERT: L 487 MET cc_start: 0.5192 (mtm) cc_final: 0.4913 (mtm) REVERT: N 67 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7292 (mtm180) outliers start: 271 outliers final: 155 residues processed: 712 average time/residue: 0.4592 time to fit residues: 507.7265 Evaluate side-chains 590 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 416 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 684 ASN Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 418 LYS Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 62 GLN Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 298 optimal weight: 8.9990 chunk 244 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 359 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 320 optimal weight: 9.9990 chunk 356 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 128 HIS ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 649 GLN ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1111 GLN I1157 GLN J 335 GLN J 430 HIS J 519 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN L 30 HIS L 129 GLN L 362 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33011 Z= 0.254 Angle : 0.641 11.301 44949 Z= 0.339 Chirality : 0.043 0.185 5147 Planarity : 0.005 0.082 5573 Dihedral : 17.313 177.726 5440 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.85 % Rotamer: Outliers : 7.83 % Allowed : 26.67 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.03 % 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: -2.61 (0.12), residues: 3875 helix: -1.02 (0.12), residues: 1563 sheet: -1.90 (0.26), residues: 363 loop : -2.32 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 997 HIS 0.004 0.001 HIS L 600 PHE 0.020 0.001 PHE L 401 TYR 0.017 0.002 TYR G 177 ARG 0.005 0.000 ARG J1341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 423 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 147 GLN cc_start: 0.8188 (tt0) cc_final: 0.7919 (tt0) REVERT: G 208 ASN cc_start: 0.7730 (p0) cc_final: 0.7321 (p0) REVERT: I 202 ARG cc_start: 0.6899 (ptt90) cc_final: 0.6370 (ptp-110) REVERT: I 239 MET cc_start: 0.5206 (ppp) cc_final: 0.4295 (ttp) REVERT: I 330 HIS cc_start: 0.0593 (OUTLIER) cc_final: 0.0246 (m170) REVERT: I 386 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6621 (tp30) REVERT: I 453 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8351 (tt) REVERT: I 496 LYS cc_start: 0.7344 (tptm) cc_final: 0.6876 (ttpp) REVERT: I 498 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7395 (pt) REVERT: I 592 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7682 (ptm160) REVERT: I 646 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.7579 (t) REVERT: I 791 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8294 (tt) REVERT: I 894 GLN cc_start: 0.6199 (mt0) cc_final: 0.5780 (mt0) REVERT: I 941 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7129 (mptt) REVERT: I 997 TRP cc_start: 0.5943 (m-10) cc_final: 0.5355 (m-90) REVERT: I 1085 MET cc_start: 0.8406 (mmm) cc_final: 0.7331 (mmm) REVERT: I 1129 ASN cc_start: 0.8082 (t0) cc_final: 0.7843 (t0) REVERT: I 1188 ASP cc_start: 0.7674 (t0) cc_final: 0.7438 (t0) REVERT: I 1238 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8536 (mt) REVERT: I 1239 VAL cc_start: 0.8882 (p) cc_final: 0.8669 (p) REVERT: J 137 ARG cc_start: 0.6898 (mtm180) cc_final: 0.6283 (mtp85) REVERT: J 163 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7208 (pt0) REVERT: J 201 LEU cc_start: 0.6182 (mm) cc_final: 0.5629 (tp) REVERT: J 203 GLU cc_start: 0.6037 (mt-10) cc_final: 0.5679 (mt-10) REVERT: J 204 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.4680 (pm20) REVERT: J 322 ARG cc_start: 0.5893 (ptp-110) cc_final: 0.5458 (ptp-110) REVERT: J 402 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5045 (tm-30) REVERT: J 443 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: J 489 ASN cc_start: 0.7493 (m-40) cc_final: 0.6768 (p0) REVERT: J 664 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7727 (mt) REVERT: J 709 ARG cc_start: 0.5791 (OUTLIER) cc_final: 0.4672 (tpm-80) REVERT: J 866 GLU cc_start: 0.6682 (mp0) cc_final: 0.6399 (mp0) REVERT: J 932 MET cc_start: 0.6498 (ptm) cc_final: 0.6233 (ptm) REVERT: J 1061 VAL cc_start: 0.0730 (OUTLIER) cc_final: 0.0038 (m) REVERT: J 1244 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7614 (mm-40) REVERT: J 1261 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8399 (pp) REVERT: K 25 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7815 (ttp-110) REVERT: K 53 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6717 (mt-10) REVERT: L 90 GLU cc_start: 0.1986 (OUTLIER) cc_final: 0.1109 (mm-30) REVERT: L 99 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6584 (tpt170) REVERT: L 121 LYS cc_start: 0.7117 (ptpp) cc_final: 0.6457 (tppt) REVERT: L 413 MET cc_start: 0.7267 (mtm) cc_final: 0.6864 (tmm) REVERT: L 476 ARG cc_start: 0.4780 (OUTLIER) cc_final: 0.3149 (mtm180) REVERT: L 487 MET cc_start: 0.5007 (mtm) cc_final: 0.4766 (mtm) REVERT: L 538 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: N 67 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7309 (mtm180) outliers start: 260 outliers final: 170 residues processed: 649 average time/residue: 0.4613 time to fit residues: 469.8124 Evaluate side-chains 583 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 393 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 592 ARG Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 528 LEU Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 360 optimal weight: 0.9990 chunk 381 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1157 GLN J 435 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 33011 Z= 0.333 Angle : 0.674 12.279 44949 Z= 0.354 Chirality : 0.045 0.176 5147 Planarity : 0.005 0.082 5573 Dihedral : 17.171 177.562 5409 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.95 % Favored : 91.95 % Rotamer: Outliers : 9.09 % Allowed : 26.40 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.05 % 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: -2.34 (0.13), residues: 3875 helix: -0.64 (0.13), residues: 1556 sheet: -1.71 (0.27), residues: 355 loop : -2.32 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 997 HIS 0.006 0.001 HIS L 600 PHE 0.021 0.002 PHE L 610 TYR 0.026 0.002 TYR I1229 ARG 0.005 0.001 ARG J1341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 415 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 208 ASN cc_start: 0.7796 (p0) cc_final: 0.7401 (p0) REVERT: I 330 HIS cc_start: 0.0680 (OUTLIER) cc_final: 0.0262 (m170) REVERT: I 379 GLU cc_start: 0.7703 (tp30) cc_final: 0.6442 (mp0) REVERT: I 386 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6595 (tp30) REVERT: I 496 LYS cc_start: 0.7200 (tptm) cc_final: 0.6720 (ttpp) REVERT: I 498 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7501 (pt) REVERT: I 646 SER cc_start: 0.7624 (OUTLIER) cc_final: 0.7293 (t) REVERT: I 791 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8315 (tt) REVERT: I 894 GLN cc_start: 0.6242 (mt0) cc_final: 0.5958 (mt0) REVERT: I 941 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7222 (mptt) REVERT: I 1085 MET cc_start: 0.8464 (mmm) cc_final: 0.7370 (mmm) REVERT: I 1129 ASN cc_start: 0.8122 (t0) cc_final: 0.7881 (t0) REVERT: I 1188 ASP cc_start: 0.7699 (t0) cc_final: 0.7435 (t0) REVERT: J 137 ARG cc_start: 0.6791 (mtm180) cc_final: 0.6289 (mtp85) REVERT: J 163 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: J 201 LEU cc_start: 0.6055 (mm) cc_final: 0.5602 (tp) REVERT: J 235 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: J 402 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5101 (tm-30) REVERT: J 443 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: J 489 ASN cc_start: 0.7529 (m-40) cc_final: 0.6802 (p0) REVERT: J 664 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7759 (mt) REVERT: J 866 GLU cc_start: 0.6664 (mp0) cc_final: 0.6367 (mp0) REVERT: J 925 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6591 (tm-30) REVERT: J 932 MET cc_start: 0.6485 (ptm) cc_final: 0.6245 (ptm) REVERT: J 1061 VAL cc_start: 0.0657 (OUTLIER) cc_final: -0.0037 (m) REVERT: J 1244 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7558 (mm-40) REVERT: J 1261 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8391 (pp) REVERT: K 53 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6805 (mt-10) REVERT: L 90 GLU cc_start: 0.1997 (OUTLIER) cc_final: 0.1127 (mm-30) REVERT: L 99 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6623 (tpt170) REVERT: L 121 LYS cc_start: 0.7148 (ptpp) cc_final: 0.6615 (tppt) REVERT: L 364 ARG cc_start: 0.5947 (mtm180) cc_final: 0.5476 (mtm-85) REVERT: L 413 MET cc_start: 0.7080 (mtm) cc_final: 0.6691 (tmm) REVERT: L 476 ARG cc_start: 0.4788 (OUTLIER) cc_final: 0.3121 (mtt180) REVERT: L 487 MET cc_start: 0.4973 (mtm) cc_final: 0.4687 (mtm) REVERT: L 538 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: L 593 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6694 (ttpp) REVERT: L 610 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.6325 (t80) REVERT: N 67 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7516 (mtm180) outliers start: 302 outliers final: 215 residues processed: 677 average time/residue: 0.4769 time to fit residues: 510.6291 Evaluate side-chains 623 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 390 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 222 THR Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 516 ASP Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 528 LEU Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 593 LYS Chi-restraints excluded: chain L residue 599 ARG Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain L residue 610 PHE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 325 optimal weight: 7.9990 chunk 263 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1157 GLN J 341 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 910 ASN ** J 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1367 GLN L 242 HIS N 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 33011 Z= 0.491 Angle : 0.777 14.018 44949 Z= 0.406 Chirality : 0.049 0.221 5147 Planarity : 0.006 0.081 5573 Dihedral : 17.325 177.115 5405 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.03 % Favored : 90.86 % Rotamer: Outliers : 10.14 % Allowed : 26.49 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.65 % Twisted General : 0.08 % 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: -2.47 (0.13), residues: 3875 helix: -0.70 (0.13), residues: 1556 sheet: -1.86 (0.26), residues: 372 loop : -2.42 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 807 HIS 0.007 0.002 HIS I 447 PHE 0.023 0.002 PHE J1325 TYR 0.030 0.003 TYR I1229 ARG 0.006 0.001 ARG I 994 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 407 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 208 ASN cc_start: 0.7905 (p0) cc_final: 0.7507 (p0) REVERT: I 84 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6284 (mt-10) REVERT: I 315 MET cc_start: 0.4013 (ptt) cc_final: 0.3651 (tpp) REVERT: I 330 HIS cc_start: 0.0853 (OUTLIER) cc_final: 0.0367 (m170) REVERT: I 378 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6437 (ttp80) REVERT: I 379 GLU cc_start: 0.7850 (tp30) cc_final: 0.6386 (mp0) REVERT: I 386 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6595 (tp30) REVERT: I 496 LYS cc_start: 0.7207 (tptm) cc_final: 0.6675 (ttpp) REVERT: I 498 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7637 (pt) REVERT: I 580 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: I 894 GLN cc_start: 0.6189 (mt0) cc_final: 0.5663 (mt0) REVERT: I 941 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7206 (mptt) REVERT: I 996 ARG cc_start: 0.6853 (mmp-170) cc_final: 0.6484 (tpt-90) REVERT: I 1085 MET cc_start: 0.8498 (mmm) cc_final: 0.7418 (mmm) REVERT: I 1129 ASN cc_start: 0.8124 (t0) cc_final: 0.7905 (t0) REVERT: I 1188 ASP cc_start: 0.7749 (t0) cc_final: 0.7547 (t0) REVERT: J 96 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7129 (pttp) REVERT: J 137 ARG cc_start: 0.6905 (mtm180) cc_final: 0.6311 (mtp85) REVERT: J 163 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7144 (pt0) REVERT: J 201 LEU cc_start: 0.6140 (mm) cc_final: 0.5676 (tp) REVERT: J 235 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: J 341 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6379 (t0) REVERT: J 402 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5249 (tm-30) REVERT: J 443 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: J 479 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8063 (mt-10) REVERT: J 489 ASN cc_start: 0.7585 (m-40) cc_final: 0.6840 (p0) REVERT: J 981 GLU cc_start: 0.4494 (OUTLIER) cc_final: 0.4024 (mt-10) REVERT: J 1061 VAL cc_start: 0.1640 (OUTLIER) cc_final: 0.1063 (p) REVERT: J 1244 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7572 (mm-40) REVERT: J 1261 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8367 (pp) REVERT: K 51 LEU cc_start: 0.8500 (mt) cc_final: 0.8281 (mt) REVERT: K 53 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7033 (mt-10) REVERT: K 74 GLU cc_start: 0.6288 (mp0) cc_final: 0.5854 (mp0) REVERT: L 78 GLU cc_start: 0.3858 (OUTLIER) cc_final: 0.2937 (mm-30) REVERT: L 90 GLU cc_start: 0.1780 (OUTLIER) cc_final: 0.0733 (mm-30) REVERT: L 99 ARG cc_start: 0.7285 (mtt180) cc_final: 0.6713 (tpt170) REVERT: L 121 LYS cc_start: 0.7132 (ptpp) cc_final: 0.6648 (tppt) REVERT: L 235 ILE cc_start: 0.1692 (OUTLIER) cc_final: 0.1484 (mt) REVERT: L 364 ARG cc_start: 0.6116 (mtm180) cc_final: 0.5740 (mtm-85) REVERT: L 393 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6405 (mmtt) REVERT: L 413 MET cc_start: 0.7081 (mtm) cc_final: 0.6721 (tmm) REVERT: L 476 ARG cc_start: 0.5041 (OUTLIER) cc_final: 0.3223 (mtt180) REVERT: L 487 MET cc_start: 0.5015 (mtm) cc_final: 0.4696 (mtm) REVERT: L 489 MET cc_start: 0.5706 (OUTLIER) cc_final: 0.5173 (mmt) REVERT: L 593 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6526 (ttpp) REVERT: N 67 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7803 (mtm180) outliers start: 337 outliers final: 251 residues processed: 701 average time/residue: 0.4569 time to fit residues: 506.3074 Evaluate side-chains 647 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 373 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 222 THR Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 740 GLU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 952 GLN Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1286 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 341 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 585 LYS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 721 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 981 GLU Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1134 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1226 VAL Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 78 GLU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 330 LEU Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 450 ILE Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 516 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 528 LEU Chi-restraints excluded: chain L residue 529 GLU Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 539 SER Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 593 LYS Chi-restraints excluded: chain L residue 599 ARG Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 6 ASP Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 0.0980 chunk 343 optimal weight: 30.0000 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 382 optimal weight: 0.7980 chunk 317 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 554 HIS ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 767 GLN ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 435 GLN J 519 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 921 GLN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1244 GLN J1326 GLN J1366 HIS L 49 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33011 Z= 0.170 Angle : 0.605 10.994 44949 Z= 0.317 Chirality : 0.042 0.166 5147 Planarity : 0.004 0.080 5573 Dihedral : 16.888 177.732 5402 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 6.62 % Allowed : 29.65 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.91 (0.13), residues: 3875 helix: -0.16 (0.13), residues: 1573 sheet: -1.68 (0.28), residues: 337 loop : -2.17 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP I 997 HIS 0.004 0.001 HIS J 865 PHE 0.018 0.001 PHE L 610 TYR 0.019 0.001 TYR I 810 ARG 0.006 0.000 ARG I 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 441 time to evaluate : 4.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 208 ASN cc_start: 0.7765 (p0) cc_final: 0.7409 (p0) REVERT: I 193 ASN cc_start: 0.6759 (m-40) cc_final: 0.6318 (m-40) REVERT: I 239 MET cc_start: 0.5447 (ppp) cc_final: 0.4099 (ttp) REVERT: I 330 HIS cc_start: 0.0454 (OUTLIER) cc_final: 0.0158 (m170) REVERT: I 386 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6526 (tp30) REVERT: I 494 ASN cc_start: 0.6073 (OUTLIER) cc_final: 0.5219 (p0) REVERT: I 496 LYS cc_start: 0.7455 (tptm) cc_final: 0.6963 (ttpp) REVERT: I 498 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7408 (pt) REVERT: I 941 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7195 (mptt) REVERT: I 1022 LYS cc_start: 0.4228 (OUTLIER) cc_final: 0.3937 (ptmt) REVERT: I 1073 LYS cc_start: 0.7947 (ptpt) cc_final: 0.7745 (ptpt) REVERT: I 1085 MET cc_start: 0.8379 (mmm) cc_final: 0.6707 (mmm) REVERT: I 1129 ASN cc_start: 0.8108 (t0) cc_final: 0.7891 (t0) REVERT: I 1188 ASP cc_start: 0.7679 (t0) cc_final: 0.7358 (t0) REVERT: I 1238 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8541 (mt) REVERT: I 1239 VAL cc_start: 0.8882 (p) cc_final: 0.8665 (p) REVERT: J 38 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8971 (t) REVERT: J 114 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7542 (tp) REVERT: J 137 ARG cc_start: 0.6621 (mtm180) cc_final: 0.6235 (mtp85) REVERT: J 163 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7189 (pt0) REVERT: J 201 LEU cc_start: 0.6215 (mm) cc_final: 0.5754 (tp) REVERT: J 252 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8190 (tp) REVERT: J 365 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: J 402 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.5106 (tm-30) REVERT: J 443 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: J 489 ASN cc_start: 0.7053 (m-40) cc_final: 0.6454 (p0) REVERT: J 932 MET cc_start: 0.6472 (ptm) cc_final: 0.6209 (ptm) REVERT: J 1061 VAL cc_start: 0.1736 (OUTLIER) cc_final: 0.1091 (m) REVERT: J 1095 MET cc_start: 0.1645 (mtt) cc_final: 0.1282 (mmp) REVERT: J 1104 LYS cc_start: 0.2736 (OUTLIER) cc_final: 0.1939 (mmmt) REVERT: J 1241 TYR cc_start: 0.8462 (m-80) cc_final: 0.8154 (m-10) REVERT: J 1343 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5150 (mm-30) REVERT: K 47 THR cc_start: 0.7927 (p) cc_final: 0.7676 (p) REVERT: K 53 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6672 (mt-10) REVERT: L 90 GLU cc_start: 0.2156 (OUTLIER) cc_final: 0.1125 (mm-30) REVERT: L 99 ARG cc_start: 0.7322 (mtt180) cc_final: 0.6755 (tpt170) REVERT: L 121 LYS cc_start: 0.6932 (ptpp) cc_final: 0.6633 (tppt) REVERT: L 218 ARG cc_start: 0.4542 (mmp80) cc_final: 0.3408 (tpp-160) REVERT: L 364 ARG cc_start: 0.6021 (mtm180) cc_final: 0.5640 (mtm-85) REVERT: L 413 MET cc_start: 0.7130 (mtm) cc_final: 0.6789 (tmm) REVERT: L 460 ILE cc_start: 0.8399 (mt) cc_final: 0.8044 (tp) REVERT: L 476 ARG cc_start: 0.4605 (OUTLIER) cc_final: 0.3043 (mtt180) REVERT: L 487 MET cc_start: 0.4991 (mtm) cc_final: 0.4726 (mtm) REVERT: L 514 ASP cc_start: 0.1706 (OUTLIER) cc_final: 0.1116 (m-30) REVERT: L 593 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6655 (ttpp) REVERT: N 67 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7568 (mtm180) outliers start: 220 outliers final: 142 residues processed: 631 average time/residue: 0.4863 time to fit residues: 486.3434 Evaluate side-chains 561 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 399 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 593 LYS Chi-restraints excluded: chain L residue 599 ARG Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 279 optimal weight: 30.0000 chunk 216 optimal weight: 4.9990 chunk 321 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 380 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 GLN I 31 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 767 GLN I 955 GLN J 435 GLN J 519 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33011 Z= 0.262 Angle : 0.637 11.365 44949 Z= 0.333 Chirality : 0.043 0.202 5147 Planarity : 0.005 0.082 5573 Dihedral : 16.750 177.599 5367 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.56 % Favored : 92.34 % Rotamer: Outliers : 6.98 % Allowed : 29.44 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.78 (0.13), residues: 3875 helix: -0.04 (0.13), residues: 1571 sheet: -1.58 (0.27), residues: 357 loop : -2.11 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 997 HIS 0.004 0.001 HIS G 160 PHE 0.021 0.002 PHE L 221 TYR 0.018 0.002 TYR I 810 ARG 0.007 0.000 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 409 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: G 208 ASN cc_start: 0.7812 (p0) cc_final: 0.7450 (p0) REVERT: I 124 MET cc_start: 0.6999 (ptm) cc_final: 0.6595 (ptm) REVERT: I 193 ASN cc_start: 0.6770 (m-40) cc_final: 0.6301 (m-40) REVERT: I 232 ILE cc_start: 0.5784 (OUTLIER) cc_final: 0.5137 (pt) REVERT: I 330 HIS cc_start: 0.0465 (OUTLIER) cc_final: 0.0192 (m170) REVERT: I 386 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6465 (tp30) REVERT: I 439 LYS cc_start: 0.7971 (mttp) cc_final: 0.7540 (tppt) REVERT: I 496 LYS cc_start: 0.7336 (tptm) cc_final: 0.6805 (ttpp) REVERT: I 498 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7443 (pt) REVERT: I 805 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8040 (ptm) REVERT: I 941 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7159 (mptt) REVERT: I 1022 LYS cc_start: 0.3976 (OUTLIER) cc_final: 0.3615 (ptmt) REVERT: I 1085 MET cc_start: 0.8403 (mmm) cc_final: 0.6681 (mmm) REVERT: I 1188 ASP cc_start: 0.7899 (t0) cc_final: 0.7624 (t0) REVERT: I 1238 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8530 (mt) REVERT: I 1239 VAL cc_start: 0.8938 (p) cc_final: 0.8685 (p) REVERT: J 137 ARG cc_start: 0.6695 (mtm180) cc_final: 0.6254 (mtp85) REVERT: J 163 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: J 201 LEU cc_start: 0.6200 (mm) cc_final: 0.5718 (tp) REVERT: J 204 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6074 (tm-30) REVERT: J 235 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7370 (pm20) REVERT: J 402 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5134 (tm-30) REVERT: J 443 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: J 489 ASN cc_start: 0.7204 (m-40) cc_final: 0.6599 (p0) REVERT: J 866 GLU cc_start: 0.6409 (mp0) cc_final: 0.6193 (mp0) REVERT: J 932 MET cc_start: 0.6383 (ptm) cc_final: 0.6146 (ptm) REVERT: J 1061 VAL cc_start: 0.1709 (OUTLIER) cc_final: 0.1055 (m) REVERT: J 1095 MET cc_start: 0.1695 (mtt) cc_final: 0.1291 (mmp) REVERT: J 1104 LYS cc_start: 0.2923 (OUTLIER) cc_final: 0.2246 (mmmt) REVERT: J 1241 TYR cc_start: 0.8535 (m-80) cc_final: 0.8204 (m-10) REVERT: K 53 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6715 (mt-10) REVERT: K 74 GLU cc_start: 0.6213 (mp0) cc_final: 0.5752 (mp0) REVERT: L 90 GLU cc_start: 0.1995 (OUTLIER) cc_final: 0.1122 (mm-30) REVERT: L 99 ARG cc_start: 0.7384 (mtt180) cc_final: 0.6745 (tpt170) REVERT: L 121 LYS cc_start: 0.7142 (ptpp) cc_final: 0.6753 (tppt) REVERT: L 218 ARG cc_start: 0.4527 (mmp80) cc_final: 0.4239 (mmp80) REVERT: L 365 MET cc_start: 0.6086 (ttt) cc_final: 0.5860 (ttt) REVERT: L 413 MET cc_start: 0.7128 (mtm) cc_final: 0.6825 (tmm) REVERT: L 414 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7010 (mptt) REVERT: L 476 ARG cc_start: 0.4640 (OUTLIER) cc_final: 0.3038 (mtm180) REVERT: L 487 MET cc_start: 0.4915 (mtm) cc_final: 0.4609 (mtm) REVERT: L 593 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6673 (ttpp) REVERT: N 67 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7593 (mtm180) outliers start: 232 outliers final: 175 residues processed: 610 average time/residue: 0.4473 time to fit residues: 430.8581 Evaluate side-chains 586 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 392 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 488 ASN Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 28 ARG Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 414 LYS Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 539 SER Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 593 LYS Chi-restraints excluded: chain L residue 599 ARG Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 299 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 GLN ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33011 Z= 0.266 Angle : 0.641 11.480 44949 Z= 0.334 Chirality : 0.044 0.215 5147 Planarity : 0.005 0.079 5573 Dihedral : 16.668 177.796 5360 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.66 % Favored : 92.23 % Rotamer: Outliers : 7.41 % Allowed : 28.96 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.73 (0.13), residues: 3875 helix: 0.01 (0.13), residues: 1566 sheet: -1.58 (0.28), residues: 357 loop : -2.08 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 997 HIS 0.004 0.001 HIS M 276 PHE 0.030 0.002 PHE L 221 TYR 0.024 0.002 TYR I1229 ARG 0.010 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 408 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: G 208 ASN cc_start: 0.7794 (p0) cc_final: 0.7441 (p0) REVERT: I 23 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: I 124 MET cc_start: 0.7105 (ptm) cc_final: 0.6812 (ptt) REVERT: I 193 ASN cc_start: 0.6759 (m-40) cc_final: 0.6277 (m-40) REVERT: I 201 ARG cc_start: 0.6681 (ttm110) cc_final: 0.6265 (ttm110) REVERT: I 232 ILE cc_start: 0.5784 (OUTLIER) cc_final: 0.5100 (pt) REVERT: I 239 MET cc_start: 0.5534 (ppp) cc_final: 0.4108 (ttp) REVERT: I 253 PHE cc_start: 0.5511 (t80) cc_final: 0.5064 (m-80) REVERT: I 330 HIS cc_start: 0.0369 (OUTLIER) cc_final: 0.0122 (m170) REVERT: I 378 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.5949 (ttp80) REVERT: I 386 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6477 (tp30) REVERT: I 436 ARG cc_start: 0.7667 (tpt90) cc_final: 0.7466 (tpt90) REVERT: I 439 LYS cc_start: 0.7970 (mttp) cc_final: 0.7546 (tppt) REVERT: I 492 MET cc_start: 0.6000 (ptp) cc_final: 0.5471 (ptp) REVERT: I 496 LYS cc_start: 0.7336 (tptm) cc_final: 0.6800 (ttpp) REVERT: I 498 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7326 (pt) REVERT: I 805 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8048 (ptm) REVERT: I 941 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7139 (mptt) REVERT: I 1022 LYS cc_start: 0.4203 (OUTLIER) cc_final: 0.3877 (ptmt) REVERT: I 1085 MET cc_start: 0.8404 (mmm) cc_final: 0.6691 (mmm) REVERT: I 1188 ASP cc_start: 0.7824 (t0) cc_final: 0.7566 (t0) REVERT: I 1238 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8527 (mt) REVERT: I 1239 VAL cc_start: 0.8952 (p) cc_final: 0.8684 (p) REVERT: J 137 ARG cc_start: 0.6720 (mtm180) cc_final: 0.6275 (mtp85) REVERT: J 163 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: J 201 LEU cc_start: 0.6250 (mm) cc_final: 0.5734 (tp) REVERT: J 204 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6078 (tm-30) REVERT: J 235 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: J 252 LEU cc_start: 0.8601 (tp) cc_final: 0.8309 (tp) REVERT: J 402 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5153 (tm-30) REVERT: J 443 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: J 479 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7993 (mt-10) REVERT: J 489 ASN cc_start: 0.7119 (m-40) cc_final: 0.6486 (p0) REVERT: J 555 TYR cc_start: 0.8052 (m-10) cc_final: 0.7803 (m-10) REVERT: J 818 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6266 (mm-30) REVERT: J 866 GLU cc_start: 0.6411 (mp0) cc_final: 0.6191 (mp0) REVERT: J 932 MET cc_start: 0.6416 (ptm) cc_final: 0.6168 (ptm) REVERT: J 1025 MET cc_start: 0.4059 (OUTLIER) cc_final: 0.3169 (mmt) REVERT: J 1061 VAL cc_start: 0.1641 (OUTLIER) cc_final: 0.1011 (m) REVERT: J 1095 MET cc_start: 0.1706 (mtt) cc_final: 0.1304 (mmp) REVERT: J 1104 LYS cc_start: 0.2842 (OUTLIER) cc_final: 0.2165 (mmmt) REVERT: J 1241 TYR cc_start: 0.8542 (m-80) cc_final: 0.8234 (m-10) REVERT: J 1343 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.4833 (mm-30) REVERT: K 53 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6634 (mt-10) REVERT: K 74 GLU cc_start: 0.6272 (mp0) cc_final: 0.5857 (mp0) REVERT: L 90 GLU cc_start: 0.2215 (OUTLIER) cc_final: 0.1217 (mm-30) REVERT: L 99 ARG cc_start: 0.7389 (mtt180) cc_final: 0.6680 (tpt170) REVERT: L 121 LYS cc_start: 0.7129 (ptpp) cc_final: 0.6739 (tppt) REVERT: L 288 MET cc_start: 0.1458 (OUTLIER) cc_final: 0.0659 (tpp) REVERT: L 413 MET cc_start: 0.7044 (mtm) cc_final: 0.6826 (tmm) REVERT: L 414 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.7058 (mptt) REVERT: L 418 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7280 (tttm) REVERT: L 476 ARG cc_start: 0.4673 (OUTLIER) cc_final: 0.2990 (mtm180) REVERT: L 487 MET cc_start: 0.4914 (mtm) cc_final: 0.4618 (mtm) REVERT: L 538 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: N 67 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7587 (mtm180) outliers start: 246 outliers final: 194 residues processed: 613 average time/residue: 0.4600 time to fit residues: 444.0022 Evaluate side-chains 611 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 391 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 671 LEU Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 952 GLN Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 414 LYS Chi-restraints excluded: chain L residue 418 LYS Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 525 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 539 SER Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 599 ARG Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 20.0000 chunk 364 optimal weight: 7.9990 chunk 332 optimal weight: 0.0370 chunk 354 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 320 optimal weight: 6.9990 chunk 335 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1257 GLN J 435 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33011 Z= 0.245 Angle : 0.630 11.840 44949 Z= 0.329 Chirality : 0.043 0.217 5147 Planarity : 0.005 0.079 5573 Dihedral : 16.602 178.022 5358 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.69 % Favored : 92.21 % Rotamer: Outliers : 7.25 % Allowed : 29.26 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.66 (0.13), residues: 3875 helix: 0.06 (0.13), residues: 1572 sheet: -1.52 (0.28), residues: 356 loop : -2.05 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 997 HIS 0.004 0.001 HIS M 276 PHE 0.014 0.001 PHE L 221 TYR 0.022 0.002 TYR I1229 ARG 0.010 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 399 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: G 208 ASN cc_start: 0.7783 (p0) cc_final: 0.7409 (p0) REVERT: H 233 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.5796 (p0) REVERT: I 23 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: I 124 MET cc_start: 0.6935 (ptm) cc_final: 0.6683 (ptt) REVERT: I 193 ASN cc_start: 0.6730 (m-40) cc_final: 0.6247 (m-40) REVERT: I 239 MET cc_start: 0.5517 (ppp) cc_final: 0.4011 (ttp) REVERT: I 330 HIS cc_start: 0.0313 (OUTLIER) cc_final: 0.0103 (m170) REVERT: I 378 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.5886 (ttp80) REVERT: I 386 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6464 (tp30) REVERT: I 436 ARG cc_start: 0.7614 (tpt90) cc_final: 0.7352 (tpt90) REVERT: I 439 LYS cc_start: 0.7969 (mttp) cc_final: 0.7580 (tppt) REVERT: I 492 MET cc_start: 0.5976 (ptp) cc_final: 0.5596 (ptp) REVERT: I 494 ASN cc_start: 0.6046 (OUTLIER) cc_final: 0.5031 (p0) REVERT: I 496 LYS cc_start: 0.7332 (tptm) cc_final: 0.6788 (ttpp) REVERT: I 498 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7314 (pt) REVERT: I 805 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8057 (ptm) REVERT: I 941 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7125 (mptt) REVERT: I 958 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8308 (ttmt) REVERT: I 1022 LYS cc_start: 0.4372 (OUTLIER) cc_final: 0.4046 (ptmt) REVERT: I 1085 MET cc_start: 0.8398 (mmm) cc_final: 0.6687 (mmm) REVERT: I 1188 ASP cc_start: 0.7855 (t0) cc_final: 0.7570 (t0) REVERT: I 1238 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8548 (mt) REVERT: I 1239 VAL cc_start: 0.8930 (p) cc_final: 0.8680 (p) REVERT: J 137 ARG cc_start: 0.6741 (mtm180) cc_final: 0.6288 (mtp85) REVERT: J 163 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: J 201 LEU cc_start: 0.6167 (mm) cc_final: 0.5719 (tp) REVERT: J 204 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6104 (tm-30) REVERT: J 235 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: J 252 LEU cc_start: 0.8538 (tp) cc_final: 0.8231 (tp) REVERT: J 402 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5143 (tm-30) REVERT: J 443 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: J 489 ASN cc_start: 0.7330 (m-40) cc_final: 0.6613 (p0) REVERT: J 818 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6140 (mm-30) REVERT: J 866 GLU cc_start: 0.6388 (mp0) cc_final: 0.6160 (mp0) REVERT: J 932 MET cc_start: 0.6428 (ptm) cc_final: 0.6157 (ptm) REVERT: J 1025 MET cc_start: 0.4016 (OUTLIER) cc_final: 0.3141 (mmt) REVERT: J 1095 MET cc_start: 0.1693 (mtt) cc_final: 0.1316 (mmp) REVERT: J 1104 LYS cc_start: 0.3161 (OUTLIER) cc_final: 0.2476 (mmmt) REVERT: J 1283 SER cc_start: 0.8436 (t) cc_final: 0.8204 (p) REVERT: J 1343 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.4862 (mm-30) REVERT: K 53 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6705 (mt-10) REVERT: L 69 GLU cc_start: 0.2687 (OUTLIER) cc_final: 0.1713 (mp0) REVERT: L 90 GLU cc_start: 0.2213 (OUTLIER) cc_final: 0.1151 (mm-30) REVERT: L 99 ARG cc_start: 0.7383 (mtt180) cc_final: 0.6663 (tpt170) REVERT: L 116 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6082 (mt-10) REVERT: L 121 LYS cc_start: 0.7052 (ptpp) cc_final: 0.6676 (tppt) REVERT: L 413 MET cc_start: 0.7019 (mtm) cc_final: 0.6811 (tmm) REVERT: L 414 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7058 (mptt) REVERT: L 418 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7260 (tttm) REVERT: L 476 ARG cc_start: 0.4622 (OUTLIER) cc_final: 0.2928 (mtm180) outliers start: 241 outliers final: 196 residues processed: 602 average time/residue: 0.4532 time to fit residues: 427.7118 Evaluate side-chains 614 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 392 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 671 LEU Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 932 GLN Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 952 GLN Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1038 THR Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 414 LYS Chi-restraints excluded: chain L residue 418 LYS Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 539 SER Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 599 ARG Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 1.9990 chunk 375 optimal weight: 20.0000 chunk 228 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 260 optimal weight: 0.9980 chunk 393 optimal weight: 10.0000 chunk 362 optimal weight: 0.1980 chunk 313 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 GLN I 86 GLN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33011 Z= 0.235 Angle : 0.630 12.880 44949 Z= 0.328 Chirality : 0.043 0.226 5147 Planarity : 0.005 0.078 5573 Dihedral : 16.537 178.230 5357 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.43 % Favored : 92.46 % Rotamer: Outliers : 7.04 % Allowed : 29.71 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.58 (0.13), residues: 3875 helix: 0.14 (0.13), residues: 1571 sheet: -1.47 (0.28), residues: 356 loop : -2.01 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 997 HIS 0.004 0.001 HIS G 160 PHE 0.014 0.001 PHE I 464 TYR 0.026 0.002 TYR I1229 ARG 0.008 0.000 ARG I 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7750 Ramachandran restraints generated. 3875 Oldfield, 0 Emsley, 3875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 402 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: G 208 ASN cc_start: 0.7696 (p0) cc_final: 0.7354 (p0) REVERT: H 65 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6136 (tp) REVERT: H 233 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.5663 (p0) REVERT: I 124 MET cc_start: 0.6925 (ptm) cc_final: 0.6544 (ptm) REVERT: I 193 ASN cc_start: 0.6686 (m-40) cc_final: 0.6226 (m-40) REVERT: I 201 ARG cc_start: 0.6750 (ttm110) cc_final: 0.6406 (ttm110) REVERT: I 253 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.4991 (m-80) REVERT: I 378 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.5828 (ttp80) REVERT: I 386 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6468 (tp30) REVERT: I 436 ARG cc_start: 0.7582 (tpt90) cc_final: 0.7372 (tpt90) REVERT: I 439 LYS cc_start: 0.7971 (mttp) cc_final: 0.7569 (tppt) REVERT: I 492 MET cc_start: 0.5924 (ptp) cc_final: 0.5574 (ptp) REVERT: I 494 ASN cc_start: 0.5939 (OUTLIER) cc_final: 0.4828 (p0) REVERT: I 496 LYS cc_start: 0.7320 (tptm) cc_final: 0.6758 (ttpp) REVERT: I 498 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7347 (pt) REVERT: I 805 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8044 (ptm) REVERT: I 941 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7128 (mptt) REVERT: I 989 LEU cc_start: 0.5879 (tp) cc_final: 0.5624 (tp) REVERT: I 1022 LYS cc_start: 0.4354 (OUTLIER) cc_final: 0.4041 (ptmt) REVERT: I 1085 MET cc_start: 0.8395 (mmm) cc_final: 0.6675 (mmm) REVERT: I 1188 ASP cc_start: 0.7856 (t0) cc_final: 0.7571 (t0) REVERT: I 1238 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8513 (mt) REVERT: I 1239 VAL cc_start: 0.8933 (p) cc_final: 0.8683 (p) REVERT: I 1319 MET cc_start: 0.6524 (ttp) cc_final: 0.6320 (ptt) REVERT: J 137 ARG cc_start: 0.6814 (mtm180) cc_final: 0.6335 (mtp85) REVERT: J 163 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7339 (pt0) REVERT: J 201 LEU cc_start: 0.6161 (mm) cc_final: 0.5741 (tp) REVERT: J 204 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6092 (tm-30) REVERT: J 235 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: J 252 LEU cc_start: 0.8593 (tp) cc_final: 0.8283 (tp) REVERT: J 402 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5128 (tm-30) REVERT: J 443 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: J 489 ASN cc_start: 0.7143 (m-40) cc_final: 0.6403 (p0) REVERT: J 644 MET cc_start: 0.8471 (mtm) cc_final: 0.8253 (mtm) REVERT: J 818 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6125 (mm-30) REVERT: J 932 MET cc_start: 0.6421 (ptm) cc_final: 0.6152 (ptm) REVERT: J 1025 MET cc_start: 0.3989 (OUTLIER) cc_final: 0.3111 (mmt) REVERT: J 1095 MET cc_start: 0.1749 (mtt) cc_final: 0.1394 (mmp) REVERT: J 1104 LYS cc_start: 0.3131 (OUTLIER) cc_final: 0.2558 (mmmt) REVERT: J 1343 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.4878 (mm-30) REVERT: K 53 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6766 (mt-10) REVERT: L 90 GLU cc_start: 0.2017 (OUTLIER) cc_final: 0.1084 (mm-30) REVERT: L 99 ARG cc_start: 0.7388 (mtt180) cc_final: 0.6657 (tpt170) REVERT: L 116 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6071 (mt-10) REVERT: L 121 LYS cc_start: 0.7030 (ptpp) cc_final: 0.6665 (tppt) REVERT: L 413 MET cc_start: 0.7002 (mtm) cc_final: 0.6802 (tmm) REVERT: L 414 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.7019 (mptt) REVERT: L 476 ARG cc_start: 0.4597 (OUTLIER) cc_final: 0.2968 (mtm180) REVERT: L 487 MET cc_start: 0.4510 (mtm) cc_final: 0.4221 (mtm) REVERT: L 599 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.5838 (mpp80) REVERT: N 67 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7457 (ttm110) outliers start: 234 outliers final: 194 residues processed: 602 average time/residue: 0.4584 time to fit residues: 438.7790 Evaluate side-chains 606 residues out of total 3347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 387 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 180 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 378 ARG Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 494 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 639 LYS Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 783 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 845 LEU Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 868 SER Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 941 LYS Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 952 GLN Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1022 LYS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1162 SER Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1302 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 118 LYS Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1066 GLU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1104 LYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1333 THR Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 414 LYS Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 538 GLU Chi-restraints excluded: chain L residue 539 SER Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 599 ARG Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 71 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 chunk 39 optimal weight: 0.0030 chunk 57 optimal weight: 4.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135786 restraints weight = 55396.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134450 restraints weight = 86033.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.135383 restraints weight = 82992.029| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33011 Z= 0.322 Angle : 0.673 12.162 44949 Z= 0.350 Chirality : 0.045 0.218 5147 Planarity : 0.005 0.079 5573 Dihedral : 16.554 178.272 5345 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.34 % Favored : 91.56 % Rotamer: Outliers : 7.25 % Allowed : 29.62 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.69 (0.13), residues: 3875 helix: -0.02 (0.13), residues: 1583 sheet: -1.48 (0.28), residues: 355 loop : -2.03 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 997 HIS 0.005 0.001 HIS I 447 PHE 0.022 0.002 PHE I 464 TYR 0.027 0.002 TYR I1229 ARG 0.007 0.000 ARG I 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8124.51 seconds wall clock time: 145 minutes 52.98 seconds (8752.98 seconds total)