Starting phenix.real_space_refine on Fri Feb 16 16:54:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/02_2024/8csq_26967_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/02_2024/8csq_26967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/02_2024/8csq_26967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/02_2024/8csq_26967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/02_2024/8csq_26967_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/02_2024/8csq_26967_neut_updated.pdb" } resolution = 2.54 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= 0.039 sd= 1.386 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: 9 Type Number sf(0) Gaussians K 4 8.98 5 Fe 8 7.16 5 Zn 1 6.06 5 P 807 5.49 5 Mg 27 5.21 5 S 252 5.16 5 C 39883 2.51 5 N 12116 2.21 5 O 14608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 23": "OE1" <-> "OE2" Residue "0 ASP 30": "OD1" <-> "OD2" Residue "0 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 146": "OE1" <-> "OE2" Residue "0 TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 209": "OD1" <-> "OD2" Residue "1 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 138": "OD1" <-> "OD2" Residue "1 ASP 183": "OD1" <-> "OD2" Residue "3 GLU 184": "OE1" <-> "OE2" Residue "4 ASP 92": "OD1" <-> "OD2" Residue "4 GLU 114": "OE1" <-> "OE2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 299": "OE1" <-> "OE2" Residue "4 PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 411": "OD1" <-> "OD2" Residue "4 ASP 443": "OD1" <-> "OD2" Residue "4 GLU 543": "OE1" <-> "OE2" Residue "4 GLU 643": "OE1" <-> "OE2" Residue "5 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 61": "OE1" <-> "OE2" Residue "5 ASP 99": "OD1" <-> "OD2" Residue "5 ASP 132": "OD1" <-> "OD2" Residue "5 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 285": "OD1" <-> "OD2" Residue "5 ASP 287": "OD1" <-> "OD2" Residue "5 TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 313": "OE1" <-> "OE2" Residue "7 GLU 147": "OE1" <-> "OE2" Residue "7 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 228": "OE1" <-> "OE2" Residue "7 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 423": "OD1" <-> "OD2" Residue "8 ASP 101": "OD1" <-> "OD2" Residue "8 GLU 133": "OE1" <-> "OE2" Residue "8 GLU 144": "OE1" <-> "OE2" Residue "8 GLU 226": "OE1" <-> "OE2" Residue "8 PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 243": "OE1" <-> "OE2" Residue "8 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 407": "OD1" <-> "OD2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E ASP 85": "OD1" <-> "OD2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G GLU 239": "OE1" <-> "OE2" Residue "G ASP 263": "OD1" <-> "OD2" Residue "G TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 311": "OE1" <-> "OE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "J GLU 104": "OE1" <-> "OE2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "J ASP 131": "OD1" <-> "OD2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "L ASP 161": "OD1" <-> "OD2" Residue "L GLU 216": "OE1" <-> "OE2" Residue "M PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 53": "OD1" <-> "OD2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O ASP 116": "OD1" <-> "OD2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O ASP 176": "OD1" <-> "OD2" Residue "O GLU 212": "OE1" <-> "OE2" Residue "O GLU 226": "OE1" <-> "OE2" Residue "P ASP 49": "OD1" <-> "OD2" Residue "P ASP 132": "OD1" <-> "OD2" Residue "R GLU 97": "OE1" <-> "OE2" Residue "R TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R ASP 287": "OD1" <-> "OD2" Residue "R GLU 323": "OE1" <-> "OE2" Residue "S ASP 36": "OD1" <-> "OD2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 113": "OD1" <-> "OD2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "T GLU 117": "OE1" <-> "OE2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "T TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 138": "OE1" <-> "OE2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 84": "OE1" <-> "OE2" Residue "U GLU 101": "OE1" <-> "OE2" Residue "U GLU 163": "OE1" <-> "OE2" Residue "U GLU 178": "OE1" <-> "OE2" Residue "U TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 200": "OE1" <-> "OE2" Residue "V ASP 281": "OD1" <-> "OD2" Residue "V GLU 370": "OE1" <-> "OE2" Residue "V ASP 371": "OD1" <-> "OD2" Residue "W ASP 97": "OD1" <-> "OD2" Residue "W PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 111": "OD1" <-> "OD2" Residue "W ASP 130": "OD1" <-> "OD2" Residue "W TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 61": "OD1" <-> "OD2" Residue "X TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 179": "OD1" <-> "OD2" Residue "X ASP 278": "OD1" <-> "OD2" Residue "X ASP 338": "OD1" <-> "OD2" Residue "X PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 362": "OE1" <-> "OE2" Residue "X GLU 375": "OE1" <-> "OE2" Residue "X GLU 379": "OE1" <-> "OE2" Residue "Y ASP 260": "OD1" <-> "OD2" Residue "Y GLU 330": "OE1" <-> "OE2" Residue "Y GLU 335": "OE1" <-> "OE2" Residue "Y TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 6": "OE1" <-> "OE2" Residue "Z TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 21": "OE1" <-> "OE2" Residue "Z TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 315": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67706 Number of models: 1 Model: "" Number of chains: 40 Chain: "0" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1754 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "1" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2098 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Chain: "3" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 395 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "4" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4585 Classifications: {'peptide': 566} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 3 Chain: "5" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2568 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 23, 'TRANS': 295} Chain: "7" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3145 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 366} Chain breaks: 1 Chain: "8" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2543 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain: "A" Number of atoms: 17027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 17027 Classifications: {'RNA': 802} Modifications used: {'rna2p_pur': 71, 'rna2p_pyr': 57, 'rna3p_pur': 346, 'rna3p_pyr': 328} Link IDs: {'rna2p': 127, 'rna3p': 674} Chain breaks: 9 Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1789 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "C" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1042 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1838 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 839 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1724 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Chain: "G" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2384 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 10, 'TRANS': 280} Chain breaks: 1 Chain: "H" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1064 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 8, 'TRANS': 121} Chain breaks: 1 Chain: "J" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 97} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 296 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain breaks: 1 Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1363 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "M" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 913 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1570 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 21, 'TRANS': 168} Chain: "P" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "R" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2382 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain: "S" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1100 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "T" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "U" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1468 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "V" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2946 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 9, 'TRANS': 349} Chain breaks: 1 Chain: "W" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "X" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2849 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 332} Chain: "Y" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1043 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "Z" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain breaks: 1 Chain: "a" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1785 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "7" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Unusual residues: {' K': 4, ' MG': 25} Classifications: {'undetermined': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14253 SG CYS 7 404 101.559 108.438 153.209 1.00 19.70 S ATOM 13774 SG CYS 7 347 105.684 103.947 150.425 1.00 30.57 S ATOM 13669 SG CYS 7 333 99.613 105.869 148.111 1.00 19.24 S ATOM 13716 SG CYS 7 339 104.969 109.317 147.912 1.00 17.52 S ATOM 49472 SG CYS O 94 114.523 152.095 98.509 1.00 27.72 S ATOM 49558 SG CYS O 105 117.210 152.626 95.968 1.00 25.97 S ATOM 49579 SG CYS O 108 116.130 155.574 98.003 1.00 27.87 S ATOM 49867 SG CYS O 143 113.672 154.153 95.450 1.00 24.24 S ATOM 51063 SG CYS P 100 125.456 65.540 48.961 1.00 47.11 S ATOM 39614 SG CYS E 105 125.303 68.448 44.204 1.00 59.43 S ATOM 50812 SG CYS P 68 125.981 64.703 42.685 1.00 47.55 S ATOM 47417 SG CYS M 26 93.225 164.015 76.755 1.00 28.06 S ATOM 56115 SG CYS T 149 97.383 163.552 76.775 1.00 31.23 S ATOM 56043 SG CYS T 139 95.301 164.940 71.131 1.00 27.78 S ATOM 56057 SG CYS T 141 97.880 164.964 73.768 1.00 26.91 S Time building chain proxies: 26.32, per 1000 atoms: 0.39 Number of scatterers: 67706 At special positions: 0 Unit cell: (226.206, 234.702, 220.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 8 26.01 K 4 19.00 S 252 16.00 P 807 15.00 Mg 27 11.99 O 14608 8.00 N 12116 7.00 C 39883 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.54 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 201 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 100 " pdb="FE2 FES P 201 " - pdb=" SG CYS E 105 " pdb="FE2 FES P 201 " - pdb=" SG CYS P 68 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 65 " pdb=" FES T 201 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 141 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 139 " pdb="FE1 FES T 201 " - pdb=" SG CYS T 149 " pdb="FE1 FES T 201 " - pdb=" SG CYS M 26 " pdb=" SF4 7 501 " pdb="FE3 SF4 7 501 " - pdb=" SG CYS 7 333 " pdb="FE1 SF4 7 501 " - pdb=" SG CYS 7 404 " pdb="FE4 SF4 7 501 " - pdb=" SG CYS 7 339 " pdb="FE2 SF4 7 501 " - pdb=" SG CYS 7 347 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 105 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 108 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 143 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " Number of angles added : 6 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 265 helices and 36 sheets defined 46.0% alpha, 9.7% beta 229 base pairs and 396 stacking pairs defined. Time for finding SS restraints: 26.28 Creating SS restraints... Processing helix chain '0' and resid 10 through 25 Processing helix chain '0' and resid 30 through 33 No H-bonds generated for 'chain '0' and resid 30 through 33' Processing helix chain '0' and resid 52 through 59 removed outlier: 5.042A pdb=" N ALA 0 56 " --> pdb=" O ARG 0 53 " (cutoff:3.500A) Processing helix chain '0' and resid 64 through 70 removed outlier: 4.756A pdb=" N ARG 0 70 " --> pdb=" O GLN 0 66 " (cutoff:3.500A) Processing helix chain '0' and resid 72 through 75 Processing helix chain '0' and resid 83 through 88 Processing helix chain '0' and resid 144 through 151 removed outlier: 5.210A pdb=" N GLU 0 148 " --> pdb=" O HIS 0 145 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR 0 151 " --> pdb=" O GLU 0 148 " (cutoff:3.500A) Processing helix chain '0' and resid 168 through 180 Processing helix chain '1' and resid 56 through 59 Processing helix chain '1' and resid 66 through 69 No H-bonds generated for 'chain '1' and resid 66 through 69' Processing helix chain '1' and resid 103 through 106 No H-bonds generated for 'chain '1' and resid 103 through 106' Processing helix chain '1' and resid 116 through 129 removed outlier: 3.647A pdb=" N LYS 1 127 " --> pdb=" O CYS 1 123 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASP 1 128 " --> pdb=" O GLU 1 124 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE 1 129 " --> pdb=" O ALA 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 146 removed outlier: 3.671A pdb=" N LYS 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 169 removed outlier: 3.908A pdb=" N ARG 1 169 " --> pdb=" O PRO 1 166 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 166 through 169' Processing helix chain '1' and resid 177 through 179 No H-bonds generated for 'chain '1' and resid 177 through 179' Processing helix chain '1' and resid 184 through 197 removed outlier: 6.779A pdb=" N GLU 1 196 " --> pdb=" O LYS 1 192 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARG 1 197 " --> pdb=" O LEU 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 215 through 233 Processing helix chain '1' and resid 238 through 241 Processing helix chain '1' and resid 257 through 272 Processing helix chain '1' and resid 287 through 301 Processing helix chain '1' and resid 306 through 320 Processing helix chain '3' and resid 154 through 180 Processing helix chain '4' and resid 69 through 76 Processing helix chain '4' and resid 100 through 123 Processing helix chain '4' and resid 125 through 127 No H-bonds generated for 'chain '4' and resid 125 through 127' Processing helix chain '4' and resid 138 through 140 No H-bonds generated for 'chain '4' and resid 138 through 140' Processing helix chain '4' and resid 154 through 162 Processing helix chain '4' and resid 166 through 179 Processing helix chain '4' and resid 185 through 198 Processing helix chain '4' and resid 243 through 250 Processing helix chain '4' and resid 256 through 268 Processing helix chain '4' and resid 272 through 284 Processing helix chain '4' and resid 291 through 303 Processing helix chain '4' and resid 309 through 325 Processing helix chain '4' and resid 332 through 362 removed outlier: 4.254A pdb=" N ARG 4 344 " --> pdb=" O LYS 4 340 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE 4 345 " --> pdb=" O CYS 4 341 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS 4 346 " --> pdb=" O LEU 4 342 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL 4 347 " --> pdb=" O ARG 4 343 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE 4 348 " --> pdb=" O ARG 4 344 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA 4 349 " --> pdb=" O PHE 4 345 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG 4 350 " --> pdb=" O HIS 4 346 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER 4 351 " --> pdb=" O VAL 4 347 " (cutoff:3.500A) Proline residue: 4 352 - end of helix Processing helix chain '4' and resid 369 through 379 Processing helix chain '4' and resid 392 through 400 Processing helix chain '4' and resid 410 through 426 removed outlier: 4.165A pdb=" N ASP 4 413 " --> pdb=" O PRO 4 410 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE 4 416 " --> pdb=" O ASP 4 413 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN 4 417 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU 4 426 " --> pdb=" O CYS 4 423 " (cutoff:3.500A) Processing helix chain '4' and resid 429 through 440 Processing helix chain '4' and resid 444 through 448 Processing helix chain '4' and resid 451 through 468 Processing helix chain '4' and resid 471 through 481 Processing helix chain '4' and resid 490 through 502 Processing helix chain '4' and resid 506 through 518 Proline residue: 4 510 - end of helix Processing helix chain '4' and resid 525 through 536 Processing helix chain '4' and resid 542 through 560 Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 589 through 601 removed outlier: 3.970A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) Processing helix chain '4' and resid 608 through 621 Processing helix chain '4' and resid 624 through 637 removed outlier: 3.567A pdb=" N PHE 4 637 " --> pdb=" O LEU 4 633 " (cutoff:3.500A) Processing helix chain '4' and resid 642 through 652 Processing helix chain '4' and resid 657 through 666 Processing helix chain '5' and resid 18 through 24 Processing helix chain '5' and resid 41 through 50 Processing helix chain '5' and resid 68 through 75 Processing helix chain '5' and resid 88 through 100 Proline residue: 5 92 - end of helix Processing helix chain '5' and resid 117 through 119 No H-bonds generated for 'chain '5' and resid 117 through 119' Processing helix chain '5' and resid 144 through 160 removed outlier: 4.170A pdb=" N THR 5 148 " --> pdb=" O PHE 5 144 " (cutoff:3.500A) Proline residue: 5 149 - end of helix Processing helix chain '5' and resid 163 through 166 Processing helix chain '5' and resid 178 through 184 Processing helix chain '5' and resid 195 through 201 Processing helix chain '5' and resid 214 through 216 No H-bonds generated for 'chain '5' and resid 214 through 216' Processing helix chain '5' and resid 242 through 253 Processing helix chain '5' and resid 260 through 267 removed outlier: 4.664A pdb=" N MET 5 266 " --> pdb=" O ARG 5 262 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU 5 267 " --> pdb=" O GLY 5 263 " (cutoff:3.500A) Processing helix chain '5' and resid 273 through 284 Processing helix chain '5' and resid 292 through 294 No H-bonds generated for 'chain '5' and resid 292 through 294' Processing helix chain '5' and resid 297 through 312 Processing helix chain '5' and resid 322 through 327 Processing helix chain '7' and resid 43 through 46 No H-bonds generated for 'chain '7' and resid 43 through 46' Processing helix chain '7' and resid 65 through 75 Processing helix chain '7' and resid 81 through 95 Processing helix chain '7' and resid 103 through 115 Processing helix chain '7' and resid 134 through 139 Processing helix chain '7' and resid 152 through 180 removed outlier: 6.191A pdb=" N ASP 7 164 " --> pdb=" O ALA 7 160 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLY 7 165 " --> pdb=" O ALA 7 161 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 198 through 207 Processing helix chain '7' and resid 221 through 231 Processing helix chain '7' and resid 268 through 270 No H-bonds generated for 'chain '7' and resid 268 through 270' Processing helix chain '7' and resid 274 through 287 Processing helix chain '7' and resid 300 through 314 Processing helix chain '7' and resid 417 through 420 No H-bonds generated for 'chain '7' and resid 417 through 420' Processing helix chain '7' and resid 422 through 430 Processing helix chain '8' and resid 87 through 98 Processing helix chain '8' and resid 102 through 107 Processing helix chain '8' and resid 112 through 115 No H-bonds generated for 'chain '8' and resid 112 through 115' Processing helix chain '8' and resid 117 through 138 removed outlier: 3.787A pdb=" N GLN 8 121 " --> pdb=" O THR 8 117 " (cutoff:3.500A) Proline residue: 8 122 - end of helix Processing helix chain '8' and resid 140 through 144 Processing helix chain '8' and resid 155 through 162 Processing helix chain '8' and resid 168 through 188 Processing helix chain '8' and resid 204 through 218 removed outlier: 3.531A pdb=" N CYS 8 215 " --> pdb=" O ALA 8 211 " (cutoff:3.500A) Processing helix chain '8' and resid 242 through 255 removed outlier: 5.860A pdb=" N SER 8 253 " --> pdb=" O GLN 8 249 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS 8 254 " --> pdb=" O LYS 8 250 " (cutoff:3.500A) Processing helix chain '8' and resid 272 through 287 Proline residue: 8 276 - end of helix removed outlier: 3.934A pdb=" N GLU 8 279 " --> pdb=" O PRO 8 276 " (cutoff:3.500A) Proline residue: 8 280 - end of helix removed outlier: 4.352A pdb=" N ALA 8 287 " --> pdb=" O ALA 8 284 " (cutoff:3.500A) Processing helix chain '8' and resid 309 through 321 removed outlier: 4.380A pdb=" N HIS 8 313 " --> pdb=" O PRO 8 309 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS 8 314 " --> pdb=" O GLY 8 310 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA 8 317 " --> pdb=" O HIS 8 313 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU 8 320 " --> pdb=" O LEU 8 316 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL 8 321 " --> pdb=" O ALA 8 317 " (cutoff:3.500A) Processing helix chain '8' and resid 326 through 334 Processing helix chain '8' and resid 353 through 361 Processing helix chain '8' and resid 363 through 368 removed outlier: 4.250A pdb=" N SER 8 368 " --> pdb=" O GLN 8 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 100 through 105 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 118 through 137 removed outlier: 3.554A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 161 removed outlier: 3.607A pdb=" N SER B 152 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TYR B 153 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 No H-bonds generated for 'chain 'B' and resid 179 through 182' Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 243 through 273 Processing helix chain 'C' and resid 21 through 24 No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 53 through 56 No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 129 through 147 Processing helix chain 'D' and resid 264 through 277 removed outlier: 3.840A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 318 through 327 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'E' and resid 15 through 31 Processing helix chain 'E' and resid 72 through 84 removed outlier: 4.657A pdb=" N GLU E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.663A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 104 through 127 Processing helix chain 'F' and resid 131 through 136 removed outlier: 4.118A pdb=" N ALA F 135 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 176 through 191 Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.600A pdb=" N HIS F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 233 removed outlier: 3.636A pdb=" N MET F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN F 233 " --> pdb=" O MET F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 92 Processing helix chain 'G' and resid 101 through 111 Processing helix chain 'G' and resid 128 through 131 No H-bonds generated for 'chain 'G' and resid 128 through 131' Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 156 through 174 Processing helix chain 'G' and resid 202 through 209 Processing helix chain 'G' and resid 215 through 230 Processing helix chain 'G' and resid 235 through 244 removed outlier: 3.861A pdb=" N PHE G 244 " --> pdb=" O PHE G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 303 No H-bonds generated for 'chain 'G' and resid 300 through 303' Processing helix chain 'G' and resid 307 through 319 Proline residue: G 316 - end of helix Processing helix chain 'G' and resid 337 through 355 removed outlier: 4.529A pdb=" N SER G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE G 355 " --> pdb=" O ALA G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 366 Processing helix chain 'H' and resid 85 through 101 Processing helix chain 'H' and resid 150 through 162 Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'J' and resid 33 through 39 Processing helix chain 'K' and resid 49 through 57 Processing helix chain 'K' and resid 108 through 116 Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 82 through 84 No H-bonds generated for 'chain 'L' and resid 82 through 84' Processing helix chain 'L' and resid 87 through 92 Processing helix chain 'L' and resid 95 through 97 No H-bonds generated for 'chain 'L' and resid 95 through 97' Processing helix chain 'L' and resid 100 through 115 Processing helix chain 'L' and resid 125 through 145 removed outlier: 3.948A pdb=" N LYS L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 173 Processing helix chain 'L' and resid 175 through 184 Processing helix chain 'L' and resid 201 through 224 Processing helix chain 'M' and resid 70 through 78 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 101 through 123 Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 62 through 68 Processing helix chain 'O' and resid 120 through 126 removed outlier: 3.690A pdb=" N GLN O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 140 No H-bonds generated for 'chain 'O' and resid 137 through 140' Processing helix chain 'O' and resid 144 through 159 Processing helix chain 'O' and resid 191 through 195 Processing helix chain 'O' and resid 201 through 203 No H-bonds generated for 'chain 'O' and resid 201 through 203' Processing helix chain 'O' and resid 210 through 219 Processing helix chain 'P' and resid 77 through 83 removed outlier: 3.647A pdb=" N GLN P 82 " --> pdb=" O GLN P 78 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 97 No H-bonds generated for 'chain 'P' and resid 94 through 97' Processing helix chain 'P' and resid 101 through 116 Processing helix chain 'P' and resid 127 through 129 No H-bonds generated for 'chain 'P' and resid 127 through 129' Processing helix chain 'R' and resid 73 through 83 Processing helix chain 'R' and resid 87 through 90 No H-bonds generated for 'chain 'R' and resid 87 through 90' Processing helix chain 'R' and resid 108 through 125 Processing helix chain 'R' and resid 146 through 148 No H-bonds generated for 'chain 'R' and resid 146 through 148' Processing helix chain 'R' and resid 167 through 169 No H-bonds generated for 'chain 'R' and resid 167 through 169' Processing helix chain 'R' and resid 186 through 196 Processing helix chain 'R' and resid 208 through 210 No H-bonds generated for 'chain 'R' and resid 208 through 210' Processing helix chain 'R' and resid 212 through 220 Processing helix chain 'R' and resid 224 through 234 Processing helix chain 'R' and resid 240 through 256 Processing helix chain 'R' and resid 259 through 261 No H-bonds generated for 'chain 'R' and resid 259 through 261' Processing helix chain 'R' and resid 268 through 278 Processing helix chain 'R' and resid 282 through 290 Processing helix chain 'R' and resid 294 through 307 Processing helix chain 'R' and resid 312 through 319 Processing helix chain 'R' and resid 324 through 334 Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'S' and resid 12 through 21 Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 66 through 77 removed outlier: 4.049A pdb=" N ILE S 70 " --> pdb=" O HIS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 108 Processing helix chain 'S' and resid 114 through 128 Processing helix chain 'T' and resid 8 through 11 Processing helix chain 'T' and resid 13 through 18 Processing helix chain 'T' and resid 39 through 50 removed outlier: 4.989A pdb=" N GLY T 43 " --> pdb=" O LEU T 40 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE T 50 " --> pdb=" O PHE T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 58 Processing helix chain 'T' and resid 95 through 106 Processing helix chain 'T' and resid 110 through 123 removed outlier: 3.842A pdb=" N LEU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 142 No H-bonds generated for 'chain 'T' and resid 140 through 142' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 161 through 164 No H-bonds generated for 'chain 'T' and resid 161 through 164' Processing helix chain 'U' and resid 36 through 38 No H-bonds generated for 'chain 'U' and resid 36 through 38' Processing helix chain 'U' and resid 50 through 87 Processing helix chain 'U' and resid 89 through 166 removed outlier: 4.018A pdb=" N LYS U 165 " --> pdb=" O GLN U 161 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN U 166 " --> pdb=" O GLU U 162 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 181 Processing helix chain 'V' and resid 32 through 35 No H-bonds generated for 'chain 'V' and resid 32 through 35' Processing helix chain 'V' and resid 38 through 41 No H-bonds generated for 'chain 'V' and resid 38 through 41' Processing helix chain 'V' and resid 50 through 62 Processing helix chain 'V' and resid 69 through 78 Processing helix chain 'V' and resid 82 through 96 removed outlier: 3.551A pdb=" N ASP V 86 " --> pdb=" O ARG V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 103 No H-bonds generated for 'chain 'V' and resid 101 through 103' Processing helix chain 'V' and resid 106 through 118 Processing helix chain 'V' and resid 122 through 130 Processing helix chain 'V' and resid 132 through 135 No H-bonds generated for 'chain 'V' and resid 132 through 135' Processing helix chain 'V' and resid 141 through 153 Processing helix chain 'V' and resid 157 through 170 Processing helix chain 'V' and resid 176 through 192 removed outlier: 4.128A pdb=" N LYS V 192 " --> pdb=" O HIS V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 198 through 214 Proline residue: V 211 - end of helix removed outlier: 3.912A pdb=" N LYS V 214 " --> pdb=" O LEU V 210 " (cutoff:3.500A) Processing helix chain 'V' and resid 218 through 238 Processing helix chain 'V' and resid 240 through 244 Processing helix chain 'V' and resid 255 through 267 Processing helix chain 'V' and resid 277 through 290 Processing helix chain 'V' and resid 323 through 344 Proline residue: V 328 - end of helix Processing helix chain 'V' and resid 352 through 404 removed outlier: 5.263A pdb=" N SER V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR V 366 " --> pdb=" O GLU V 362 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 85 Processing helix chain 'W' and resid 88 through 92 Processing helix chain 'W' and resid 131 through 133 No H-bonds generated for 'chain 'W' and resid 131 through 133' Processing helix chain 'X' and resid 56 through 58 No H-bonds generated for 'chain 'X' and resid 56 through 58' Processing helix chain 'X' and resid 61 through 63 No H-bonds generated for 'chain 'X' and resid 61 through 63' Processing helix chain 'X' and resid 72 through 78 Processing helix chain 'X' and resid 85 through 94 Processing helix chain 'X' and resid 103 through 113 Processing helix chain 'X' and resid 134 through 147 Processing helix chain 'X' and resid 158 through 162 removed outlier: 3.541A pdb=" N TRP X 161 " --> pdb=" O ALA X 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 181 through 194 removed outlier: 3.506A pdb=" N TRP X 187 " --> pdb=" O GLU X 183 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN X 190 " --> pdb=" O THR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 198 through 201 No H-bonds generated for 'chain 'X' and resid 198 through 201' Processing helix chain 'X' and resid 222 through 231 Processing helix chain 'X' and resid 233 through 253 removed outlier: 5.020A pdb=" N THR X 237 " --> pdb=" O ARG X 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP X 238 " --> pdb=" O ASN X 235 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY X 241 " --> pdb=" O ASP X 238 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE X 242 " --> pdb=" O ALA X 239 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS X 248 " --> pdb=" O LYS X 245 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN X 250 " --> pdb=" O LEU X 247 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER X 251 " --> pdb=" O LYS X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 267 No H-bonds generated for 'chain 'X' and resid 265 through 267' Processing helix chain 'X' and resid 284 through 286 No H-bonds generated for 'chain 'X' and resid 284 through 286' Processing helix chain 'X' and resid 288 through 296 removed outlier: 3.921A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 337 removed outlier: 6.869A pdb=" N LYS X 331 " --> pdb=" O GLU X 327 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLU X 332 " --> pdb=" O LEU X 328 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY X 333 " --> pdb=" O LEU X 329 " (cutoff:3.500A) Processing helix chain 'X' and resid 350 through 362 Processing helix chain 'X' and resid 374 through 384 Processing helix chain 'X' and resid 388 through 397 removed outlier: 3.920A pdb=" N TYR X 397 " --> pdb=" O ARG X 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 277 through 290 removed outlier: 3.809A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN Y 290 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 297 through 307 Processing helix chain 'Y' and resid 328 through 332 Processing helix chain 'Y' and resid 335 through 338 removed outlier: 3.520A pdb=" N LEU Y 338 " --> pdb=" O GLU Y 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 335 through 338' Processing helix chain 'Y' and resid 346 through 360 removed outlier: 3.512A pdb=" N LYS Y 360 " --> pdb=" O CYS Y 356 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 382 Processing helix chain 'Z' and resid 6 through 19 Processing helix chain 'Z' and resid 30 through 38 removed outlier: 4.066A pdb=" N VAL Z 33 " --> pdb=" O SER Z 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE Z 37 " --> pdb=" O VAL Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 67 Processing helix chain 'a' and resid 126 through 134 Processing helix chain 'a' and resid 189 through 196 removed outlier: 4.002A pdb=" N SER a 196 " --> pdb=" O LYS a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 217 through 225 Processing helix chain 'a' and resid 238 through 240 No H-bonds generated for 'chain 'a' and resid 238 through 240' Processing helix chain 'a' and resid 244 through 254 Processing helix chain 'a' and resid 316 through 325 Processing helix chain 'a' and resid 344 through 359 Processing helix chain 'a' and resid 364 through 367 Processing helix chain 'a' and resid 394 through 401 Processing helix chain 'a' and resid 403 through 423 removed outlier: 6.291A pdb=" N VAL a 407 " --> pdb=" O LYS a 404 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE a 408 " --> pdb=" O GLY a 405 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE a 423 " --> pdb=" O MET a 420 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 80 through 82 Processing sheet with id= B, first strand: chain '0' and resid 128 through 130 removed outlier: 6.013A pdb=" N ILE 0 117 " --> pdb=" O LEU 0 97 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU 0 97 " --> pdb=" O ILE 0 117 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR 0 119 " --> pdb=" O TRP 0 95 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP 0 95 " --> pdb=" O THR 0 119 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 163 through 165 Processing sheet with id= D, first strand: chain '1' and resid 150 through 153 Processing sheet with id= E, first strand: chain '5' and resid 204 through 212 removed outlier: 6.888A pdb=" N VAL 5 227 " --> pdb=" O ILE 5 209 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR 5 211 " --> pdb=" O VAL 5 225 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 5 225 " --> pdb=" O THR 5 211 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN 5 171 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR 5 58 " --> pdb=" O HIS 5 137 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE 5 139 " --> pdb=" O TYR 5 58 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR 5 60 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU 5 80 " --> pdb=" O VAL 5 59 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU 5 61 " --> pdb=" O GLU 5 80 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU 5 82 " --> pdb=" O GLU 5 61 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG 5 106 " --> pdb=" O VAL 5 83 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLU 5 85 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL 5 108 " --> pdb=" O GLU 5 85 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '7' and resid 349 through 353 removed outlier: 4.388A pdb=" N ALA 7 265 " --> pdb=" O PHE 7 192 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '7' and resid 393 through 395 Processing sheet with id= H, first strand: chain '7' and resid 327 through 331 removed outlier: 6.790A pdb=" N ILE 7 373 " --> pdb=" O PHE 7 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '8' and resid 369 through 371 removed outlier: 6.030A pdb=" N THR 8 345 " --> pdb=" O SER 8 370 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU 8 65 " --> pdb=" O VAL 8 147 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA 8 149 " --> pdb=" O LEU 8 65 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE 8 67 " --> pdb=" O ALA 8 149 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY 8 151 " --> pdb=" O PHE 8 67 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER 8 296 " --> pdb=" O ALA 8 149 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY 8 151 " --> pdb=" O SER 8 296 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N TYR 8 298 " --> pdb=" O GLY 8 151 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '8' and resid 257 through 262 removed outlier: 6.898A pdb=" N LEU 8 197 " --> pdb=" O ARG 8 258 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR 8 260 " --> pdb=" O SER 8 195 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N SER 8 195 " --> pdb=" O THR 8 260 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N MET 8 262 " --> pdb=" O MET 8 193 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N MET 8 193 " --> pdb=" O MET 8 262 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER 8 239 " --> pdb=" O VAL 8 227 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL 8 227 " --> pdb=" O SER 8 239 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.613A pdb=" N LEU B 192 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 145 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 194 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE B 195 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 220 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR B 234 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL B 223 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL B 236 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.875A pdb=" N ILE B 115 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B 109 " --> pdb=" O HIS B 113 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N HIS B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.537A pdb=" N ARG C 113 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.905A pdb=" N GLN C 156 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 254 through 261 removed outlier: 6.289A pdb=" N ALA D 246 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE D 222 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY D 248 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR D 220 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 294 through 298 Processing sheet with id= Q, first strand: chain 'D' and resid 370 through 372 removed outlier: 3.554A pdb=" N ALA D 385 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU D 372 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL D 383 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 43 through 46 removed outlier: 3.635A pdb=" N GLY E 43 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS E 11 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL E 88 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 51 through 53 Processing sheet with id= T, first strand: chain 'E' and resid 35 through 41 removed outlier: 6.891A pdb=" N ASP E 67 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU E 39 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU E 65 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 156 through 163 removed outlier: 3.515A pdb=" N LYS F 163 " --> pdb=" O ARG F 166 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 269 through 276 Processing sheet with id= W, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.182A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR H 175 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU H 76 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR H 173 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL H 78 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU H 171 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL H 80 " --> pdb=" O ALA H 169 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA H 169 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 114 through 119 Processing sheet with id= Y, first strand: chain 'J' and resid 107 through 111 removed outlier: 6.839A pdb=" N ARG J 82 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR J 65 " --> pdb=" O CYS J 80 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N CYS J 80 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR J 67 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 17 through 26 removed outlier: 6.545A pdb=" N ALA M 36 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN M 50 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU M 65 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 12 through 16 removed outlier: 8.615A pdb=" N LYS N 78 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE N 50 " --> pdb=" O LYS N 78 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU N 80 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HIS N 52 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG N 29 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL N 17 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 63 through 65 removed outlier: 6.415A pdb=" N LEU N 65 " --> pdb=" O ILE N 84 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE N 84 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 156 through 159 removed outlier: 6.541A pdb=" N LYS R 183 " --> pdb=" O VAL R 141 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL R 141 " --> pdb=" O LYS R 183 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'T' and resid 63 through 68 removed outlier: 6.696A pdb=" N TYR T 79 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET T 30 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG T 77 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL T 32 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE T 75 " --> pdb=" O VAL T 32 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'U' and resid 189 through 191 Processing sheet with id= AF, first strand: chain 'W' and resid 122 through 125 removed outlier: 3.634A pdb=" N HIS W 106 " --> pdb=" O TYR W 113 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP W 115 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE W 104 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS W 98 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY W 171 " --> pdb=" O ARG W 141 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG W 143 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU W 169 " --> pdb=" O ARG W 143 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'X' and resid 67 through 70 removed outlier: 4.370A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'X' and resid 341 through 345 removed outlier: 4.453A pdb=" N ILE X 122 " --> pdb=" O GLY X 304 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU X 258 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL X 307 " --> pdb=" O LEU X 258 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL X 260 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA X 309 " --> pdb=" O VAL X 260 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL X 262 " --> pdb=" O ALA X 309 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU X 151 " --> pdb=" O LEU X 259 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA X 261 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU X 153 " --> pdb=" O ALA X 261 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASP X 263 " --> pdb=" O LEU X 153 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE X 155 " --> pdb=" O ASP X 263 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'a' and resid 302 through 307 removed outlier: 7.982A pdb=" N SER a 231 " --> pdb=" O LYS a 303 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE a 305 " --> pdb=" O SER a 231 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU a 233 " --> pdb=" O ILE a 305 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N MET a 307 " --> pdb=" O LEU a 233 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET a 235 " --> pdb=" O MET a 307 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'a' and resid 427 through 435 removed outlier: 6.396A pdb=" N LEU a 383 " --> pdb=" O ASP a 428 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ARG a 430 " --> pdb=" O LEU a 383 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE a 385 " --> pdb=" O ARG a 430 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N SER a 432 " --> pdb=" O ILE a 385 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN a 387 " --> pdb=" O SER a 432 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LYS a 434 " --> pdb=" O GLN a 387 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU a 389 " --> pdb=" O LYS a 434 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS a 388 " --> pdb=" O THR a 372 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR a 372 " --> pdb=" O LYS a 388 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU a 390 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLN a 370 " --> pdb=" O LEU a 390 " (cutoff:3.500A) 2066 hydrogen bonds defined for protein. 5769 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 559 hydrogen bonds 1010 hydrogen bond angles 0 basepair planarities 229 basepair parallelities 396 stacking parallelities Total time for adding SS restraints: 37.96 Time building geometry restraints manager: 25.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 32666 1.43 - 1.65: 37748 1.65 - 1.87: 388 1.87 - 2.09: 0 2.09 - 2.31: 20 Bond restraints: 70822 Sorted by residual: bond pdb=" N1 GDP X 503 " pdb=" C2 GDP X 503 " ideal model delta sigma weight residual 1.337 1.558 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C6 GDP X 503 " pdb=" O6 GDP X 503 " ideal model delta sigma weight residual 1.250 1.416 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" C5 GDP X 503 " pdb=" C4 GDP X 503 " ideal model delta sigma weight residual 1.490 1.351 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C2 GDP X 503 " pdb=" N2 GDP X 503 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C2 GDP X 503 " pdb=" N3 GDP X 503 " ideal model delta sigma weight residual 1.350 1.453 -0.103 2.00e-02 2.50e+03 2.68e+01 ... (remaining 70817 not shown) Histogram of bond angle deviations from ideal: 71.74 - 85.34: 16 85.34 - 98.95: 1 98.95 - 112.55: 42600 112.55 - 126.16: 53666 126.16 - 139.77: 3284 Bond angle restraints: 99567 Sorted by residual: angle pdb=" CA PRO 8 59 " pdb=" N PRO 8 59 " pdb=" CD PRO 8 59 " ideal model delta sigma weight residual 112.00 103.30 8.70 1.40e+00 5.10e-01 3.87e+01 angle pdb=" CA PRO 7 103 " pdb=" N PRO 7 103 " pdb=" CD PRO 7 103 " ideal model delta sigma weight residual 112.00 104.39 7.61 1.40e+00 5.10e-01 2.96e+01 angle pdb=" C VAL 4 508 " pdb=" N ILE 4 509 " pdb=" CA ILE 4 509 " ideal model delta sigma weight residual 120.24 123.22 -2.98 6.30e-01 2.52e+00 2.24e+01 angle pdb=" C PHE 5 90 " pdb=" N ILE 5 91 " pdb=" CA ILE 5 91 " ideal model delta sigma weight residual 120.24 122.90 -2.66 6.30e-01 2.52e+00 1.78e+01 angle pdb=" C3' C A1330 " pdb=" O3' C A1330 " pdb=" P A A1331 " ideal model delta sigma weight residual 120.20 125.59 -5.39 1.50e+00 4.44e-01 1.29e+01 ... (remaining 99562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 41263 35.01 - 70.02: 2118 70.02 - 105.03: 330 105.03 - 140.03: 14 140.03 - 175.04: 7 Dihedral angle restraints: 43732 sinusoidal: 25408 harmonic: 18324 Sorted by residual: dihedral pdb=" CA LYS J 72 " pdb=" C LYS J 72 " pdb=" N PRO J 73 " pdb=" CA PRO J 73 " ideal model delta harmonic sigma weight residual 180.00 123.29 56.71 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" O4' C A 870 " pdb=" C1' C A 870 " pdb=" N1 C A 870 " pdb=" C2 C A 870 " ideal model delta sinusoidal sigma weight residual 200.00 33.50 166.50 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' C A1233 " pdb=" C1' C A1233 " pdb=" N1 C A1233 " pdb=" C2 C A1233 " ideal model delta sinusoidal sigma weight residual 200.00 44.18 155.82 1 1.50e+01 4.44e-03 8.16e+01 ... (remaining 43729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.210: 11634 4.210 - 8.419: 0 8.419 - 12.629: 0 12.629 - 16.838: 0 16.838 - 21.048: 4 Chirality restraints: 11638 Sorted by residual: chirality pdb="FE2 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S3 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.49 21.05 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S3 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.47 21.03 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.43 -20.98 2.00e-01 2.50e+01 1.10e+04 ... (remaining 11635 not shown) Planarity restraints: 9784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU 7 102 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO 7 103 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO 7 103 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO 7 103 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG T 160 " 0.402 9.50e-02 1.11e+02 1.80e-01 2.03e+01 pdb=" NE ARG T 160 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG T 160 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG T 160 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG T 160 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET 8 58 " -0.073 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO 8 59 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO 8 59 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO 8 59 " -0.057 5.00e-02 4.00e+02 ... (remaining 9781 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.59: 549 2.59 - 3.23: 62695 3.23 - 3.87: 143158 3.87 - 4.50: 196373 4.50 - 5.14: 285564 Nonbonded interactions: 688339 Sorted by model distance: nonbonded pdb=" OP1 C A 806 " pdb="MG MG A1709 " model vdw 1.958 2.170 nonbonded pdb=" OP1 A A 801 " pdb="MG MG A1709 " model vdw 1.961 2.170 nonbonded pdb=" OP2 A A 731 " pdb="MG MG A1714 " model vdw 1.963 2.170 nonbonded pdb=" O2' A A 738 " pdb=" O2 C A 739 " model vdw 1.965 2.440 nonbonded pdb=" OG1 THR X 135 " pdb="MG MG X 502 " model vdw 1.973 2.170 ... (remaining 688334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 15.520 Check model and map are aligned: 0.750 Set scattering table: 0.460 Process input model: 191.200 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 225.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 70822 Z= 0.266 Angle : 0.642 11.368 99567 Z= 0.344 Chirality : 0.391 21.048 11638 Planarity : 0.006 0.180 9784 Dihedral : 18.545 175.042 31838 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 6167 helix: 1.46 (0.10), residues: 2949 sheet: 0.03 (0.19), residues: 667 loop : 0.25 (0.13), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 1 239 HIS 0.013 0.001 HIS R 247 PHE 0.028 0.002 PHE 4 335 TYR 0.037 0.002 TYR 4 486 ARG 0.011 0.001 ARG T 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 988 time to evaluate : 4.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 318 ARG cc_start: 0.6996 (mmp80) cc_final: 0.6547 (mmm160) REVERT: 4 260 CYS cc_start: 0.6487 (p) cc_final: 0.6229 (p) REVERT: C 19 ARG cc_start: 0.5146 (mmt-90) cc_final: 0.4234 (tpt-90) REVERT: G 138 ILE cc_start: 0.8033 (tp) cc_final: 0.7645 (pt) REVERT: G 314 MET cc_start: 0.8609 (ttp) cc_final: 0.8237 (ttp) REVERT: G 321 ASP cc_start: 0.7277 (m-30) cc_final: 0.6749 (m-30) REVERT: J 36 MET cc_start: 0.9218 (mtp) cc_final: 0.8868 (mtp) REVERT: N 59 THR cc_start: 0.8430 (m) cc_final: 0.8195 (m) REVERT: N 105 TYR cc_start: 0.8860 (m-80) cc_final: 0.8545 (m-80) REVERT: O 62 GLU cc_start: 0.6883 (tp30) cc_final: 0.6510 (tp30) REVERT: O 164 ILE cc_start: 0.9049 (mt) cc_final: 0.8794 (mp) REVERT: O 177 PHE cc_start: 0.8856 (m-80) cc_final: 0.8640 (m-80) REVERT: O 235 MET cc_start: 0.8750 (tpp) cc_final: 0.8383 (tpt) REVERT: P 87 PHE cc_start: 0.7143 (m-80) cc_final: 0.6886 (m-80) REVERT: P 120 MET cc_start: 0.8311 (ttt) cc_final: 0.8039 (ttt) REVERT: R 116 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7054 (ttp-110) REVERT: R 277 ASN cc_start: 0.8439 (m-40) cc_final: 0.8190 (m110) REVERT: U 44 MET cc_start: 0.7605 (mmm) cc_final: 0.7373 (mmm) REVERT: V 276 CYS cc_start: 0.7484 (m) cc_final: 0.7082 (m) REVERT: W 83 MET cc_start: 0.8776 (mtt) cc_final: 0.8506 (mtt) REVERT: W 110 ASN cc_start: 0.7376 (m-40) cc_final: 0.7148 (m110) REVERT: Y 351 MET cc_start: 0.6999 (mmm) cc_final: 0.6538 (mmm) outliers start: 0 outliers final: 3 residues processed: 988 average time/residue: 1.6909 time to fit residues: 2115.3872 Evaluate side-chains 704 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 701 time to evaluate : 4.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain Z residue 63 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 584 optimal weight: 6.9990 chunk 524 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 353 optimal weight: 7.9990 chunk 280 optimal weight: 20.0000 chunk 542 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 329 optimal weight: 0.7980 chunk 403 optimal weight: 5.9990 chunk 628 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 3 158 GLN 4 175 GLN 4 189 ASN 4 326 GLN 4 417 GLN 4 540 HIS 4 545 GLN 4 602 HIS 5 171 GLN 5 208 HIS 5 229 HIS 5 294 GLN 7 60 HIS 7 69 ASN 7 98 HIS 7 144 HIS 7 290 HIS ** 7 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 400 HIS 8 83 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 313 HIS B 74 ASN B 124 HIS B 266 GLN C 57 HIS C 130 HIS G 255 GLN K 113 HIS K 119 GLN O 207 GLN R 221 GLN R 299 ASN R 308 HIS R 315 GLN R 320 GLN R 347 GLN S 47 GLN S 91 ASN S 107 GLN T 37 HIS T 85 GLN U 79 GLN U 110 GLN U 186 ASN X 159 HIS a 260 ASN a 321 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.226 70822 Z= 0.368 Angle : 0.837 51.047 99567 Z= 0.493 Chirality : 0.126 6.534 11638 Planarity : 0.005 0.076 9784 Dihedral : 19.648 167.845 19029 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.53 % Allowed : 8.82 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.11), residues: 6167 helix: 1.40 (0.09), residues: 2936 sheet: 0.33 (0.20), residues: 652 loop : 0.22 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 1 239 HIS 0.013 0.001 HIS R 247 PHE 0.027 0.002 PHE V 144 TYR 0.021 0.002 TYR V 91 ARG 0.008 0.001 ARG G 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 733 time to evaluate : 4.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 26 ASN cc_start: 0.8041 (m-40) cc_final: 0.7796 (m110) REVERT: 1 268 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: 1 288 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6683 (mt-10) REVERT: 1 318 ARG cc_start: 0.6874 (mmp80) cc_final: 0.6627 (mmp-170) REVERT: 3 163 ARG cc_start: 0.7862 (ttp-110) cc_final: 0.7320 (mtm-85) REVERT: 4 328 VAL cc_start: 0.7365 (m) cc_final: 0.7069 (t) REVERT: 4 350 ARG cc_start: 0.6664 (mtt180) cc_final: 0.6461 (mtt180) REVERT: 4 507 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: 5 96 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5913 (mtp) REVERT: B 181 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8238 (tp) REVERT: B 204 GLU cc_start: 0.7753 (mp0) cc_final: 0.7518 (mm-30) REVERT: C 19 ARG cc_start: 0.5169 (mmt-90) cc_final: 0.4137 (tpt-90) REVERT: D 330 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8454 (mmtp) REVERT: F 138 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: G 245 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7064 (tpt90) REVERT: G 286 TYR cc_start: 0.8129 (m-80) cc_final: 0.7860 (m-80) REVERT: G 314 MET cc_start: 0.8575 (ttp) cc_final: 0.8137 (ttp) REVERT: G 321 ASP cc_start: 0.7381 (m-30) cc_final: 0.7067 (m-30) REVERT: J 36 MET cc_start: 0.9197 (mtp) cc_final: 0.8815 (mtp) REVERT: O 62 GLU cc_start: 0.6863 (tp30) cc_final: 0.6517 (tp30) REVERT: O 145 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8333 (ttpt) REVERT: O 235 MET cc_start: 0.8723 (tpp) cc_final: 0.8406 (tpt) REVERT: P 87 PHE cc_start: 0.7146 (m-80) cc_final: 0.6904 (m-80) REVERT: P 131 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6461 (pptt) REVERT: R 72 ASP cc_start: 0.7052 (t70) cc_final: 0.6824 (t0) REVERT: R 112 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: R 116 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7281 (ttp-110) REVERT: R 127 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8100 (tttt) REVERT: R 133 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7360 (mm-30) REVERT: R 331 PHE cc_start: 0.7835 (t80) cc_final: 0.7475 (t80) REVERT: V 77 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7641 (t0) REVERT: V 396 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: V 398 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5822 (mt-10) REVERT: W 77 VAL cc_start: 0.6530 (t) cc_final: 0.6242 (t) REVERT: W 109 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: W 110 ASN cc_start: 0.7474 (m-40) cc_final: 0.7272 (m110) REVERT: X 227 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6544 (tp30) REVERT: Y 351 MET cc_start: 0.6999 (mmm) cc_final: 0.6678 (mmm) REVERT: Z 13 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6398 (ttm170) REVERT: Z 21 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6459 (mm-30) outliers start: 138 outliers final: 59 residues processed: 799 average time/residue: 1.6124 time to fit residues: 1646.8786 Evaluate side-chains 754 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 676 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 SER Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 183 VAL Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 262 MET Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 7 residue 317 LYS Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 117 THR Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain O residue 145 LYS Chi-restraints excluded: chain O residue 234 SER Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 131 LYS Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 334 THR Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 196 LEU Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain V residue 62 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 227 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 13 ARG Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 349 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 523 optimal weight: 20.0000 chunk 427 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 629 optimal weight: 2.9990 chunk 680 optimal weight: 9.9990 chunk 560 optimal weight: 0.9990 chunk 624 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 505 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 107 GLN 1 305 ASN ** 4 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 417 GLN 5 208 HIS 5 251 ASN 8 83 ASN ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN C 156 GLN F 147 GLN O 204 ASN R 315 GLN R 347 GLN S 47 GLN S 91 ASN S 107 GLN T 18 GLN U 186 ASN W 173 GLN a 123 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 70822 Z= 0.337 Angle : 0.800 50.553 99567 Z= 0.477 Chirality : 0.124 6.419 11638 Planarity : 0.005 0.090 9784 Dihedral : 19.563 167.865 19022 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.98 % Allowed : 10.71 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.11), residues: 6167 helix: 1.45 (0.10), residues: 2934 sheet: 0.42 (0.20), residues: 642 loop : 0.21 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 1 239 HIS 0.034 0.001 HIS H 51 PHE 0.022 0.002 PHE Y 259 TYR 0.026 0.002 TYR a 226 ARG 0.022 0.001 ARG 4 585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 699 time to evaluate : 4.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 26 ASN cc_start: 0.8082 (m-40) cc_final: 0.7828 (m110) REVERT: 0 65 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8782 (mp) REVERT: 0 192 ASN cc_start: 0.8868 (t0) cc_final: 0.8536 (t0) REVERT: 1 268 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: 1 288 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6563 (mt-10) REVERT: 3 163 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.7620 (mtp85) REVERT: 4 507 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: 4 650 MET cc_start: 0.3750 (OUTLIER) cc_final: 0.3254 (mpp) REVERT: 5 96 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.5937 (mtp) REVERT: B 181 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8363 (tp) REVERT: C 19 ARG cc_start: 0.5039 (mmt-90) cc_final: 0.4217 (tpt-90) REVERT: D 330 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8417 (mmtp) REVERT: F 179 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6874 (ptt90) REVERT: G 314 MET cc_start: 0.8547 (ttp) cc_final: 0.8086 (ttp) REVERT: G 321 ASP cc_start: 0.7371 (m-30) cc_final: 0.7019 (m-30) REVERT: J 36 MET cc_start: 0.9195 (mtp) cc_final: 0.8778 (mtp) REVERT: O 62 GLU cc_start: 0.6727 (tp30) cc_final: 0.6424 (tp30) REVERT: O 133 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8918 (mt) REVERT: O 145 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8436 (ttpt) REVERT: O 210 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: O 235 MET cc_start: 0.8771 (tpp) cc_final: 0.8468 (tpt) REVERT: P 87 PHE cc_start: 0.7200 (m-80) cc_final: 0.6952 (m-80) REVERT: P 131 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6515 (pptt) REVERT: R 72 ASP cc_start: 0.7099 (t70) cc_final: 0.6838 (t0) REVERT: R 116 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7924 (ttp80) REVERT: R 127 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8096 (tttt) REVERT: R 133 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7407 (mm-30) REVERT: R 331 PHE cc_start: 0.7855 (t80) cc_final: 0.7569 (t80) REVERT: T 9 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8573 (tp) REVERT: V 77 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7660 (t0) REVERT: V 396 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: V 398 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5825 (mt-10) REVERT: W 109 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: Y 351 MET cc_start: 0.7116 (mmm) cc_final: 0.6741 (mmm) REVERT: Z 13 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6379 (ttm170) REVERT: Z 21 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6469 (mm-30) REVERT: Z 63 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.6037 (tp40) outliers start: 162 outliers final: 65 residues processed: 783 average time/residue: 1.6432 time to fit residues: 1641.6147 Evaluate side-chains 747 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 660 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 31 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 262 MET Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 317 LYS Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 180 GLU Chi-restraints excluded: chain 8 residue 206 PHE Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 133 ILE Chi-restraints excluded: chain O residue 145 LYS Chi-restraints excluded: chain O residue 210 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 131 LYS Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 334 THR Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 196 LEU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 13 ARG Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 63 GLN Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 621 optimal weight: 0.9980 chunk 473 optimal weight: 8.9990 chunk 326 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 300 optimal weight: 0.9990 chunk 422 optimal weight: 8.9990 chunk 631 optimal weight: 7.9990 chunk 668 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 598 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 107 GLN 1 305 ASN 4 189 ASN 5 208 HIS 8 83 ASN ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 266 GLN C 116 GLN O 204 ASN R 315 GLN S 47 GLN S 91 ASN S 107 GLN U 186 ASN X 211 ASN ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 70822 Z= 0.296 Angle : 0.777 50.546 99567 Z= 0.467 Chirality : 0.123 6.381 11638 Planarity : 0.004 0.065 9784 Dihedral : 19.452 169.663 19022 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.98 % Allowed : 11.86 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.11), residues: 6167 helix: 1.57 (0.10), residues: 2931 sheet: 0.55 (0.20), residues: 625 loop : 0.25 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 3 177 HIS 0.008 0.001 HIS 7 52 PHE 0.021 0.001 PHE Y 259 TYR 0.022 0.001 TYR a 322 ARG 0.005 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 698 time to evaluate : 4.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 26 ASN cc_start: 0.8088 (m-40) cc_final: 0.7831 (m110) REVERT: 0 65 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8716 (mp) REVERT: 0 192 ASN cc_start: 0.8865 (t0) cc_final: 0.8546 (t0) REVERT: 1 268 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: 1 288 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6448 (mt-10) REVERT: 4 507 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: 4 650 MET cc_start: 0.3780 (OUTLIER) cc_final: 0.3392 (mpp) REVERT: 5 96 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5970 (mtp) REVERT: C 19 ARG cc_start: 0.4984 (mmt-90) cc_final: 0.4088 (tpt-90) REVERT: D 330 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8402 (mmtp) REVERT: F 138 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6876 (tm-30) REVERT: G 245 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7048 (tpt90) REVERT: G 267 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6448 (mtp) REVERT: G 314 MET cc_start: 0.8543 (ttp) cc_final: 0.8087 (ttp) REVERT: J 36 MET cc_start: 0.9184 (mtp) cc_final: 0.8767 (mtp) REVERT: O 62 GLU cc_start: 0.6693 (tp30) cc_final: 0.6333 (tp30) REVERT: O 145 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8431 (ttpt) REVERT: O 235 MET cc_start: 0.8876 (tpp) cc_final: 0.8504 (tpt) REVERT: P 87 PHE cc_start: 0.7232 (m-80) cc_final: 0.6979 (m-80) REVERT: P 131 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6508 (pptt) REVERT: R 72 ASP cc_start: 0.7071 (t70) cc_final: 0.6807 (t0) REVERT: R 112 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: R 127 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8069 (tttt) REVERT: R 133 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7428 (mm-30) REVERT: R 315 GLN cc_start: 0.5763 (mm-40) cc_final: 0.5507 (mm110) REVERT: R 331 PHE cc_start: 0.7836 (t80) cc_final: 0.7581 (t80) REVERT: R 344 LEU cc_start: 0.7740 (tt) cc_final: 0.7524 (tt) REVERT: T 9 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8590 (tp) REVERT: V 77 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7623 (t0) REVERT: V 358 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6420 (mm-40) REVERT: V 396 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: W 109 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6529 (mp0) REVERT: Y 351 MET cc_start: 0.7067 (mmm) cc_final: 0.6731 (mmm) REVERT: a 266 MET cc_start: 0.3644 (mmm) cc_final: 0.3130 (mmm) outliers start: 162 outliers final: 72 residues processed: 787 average time/residue: 1.6485 time to fit residues: 1655.8580 Evaluate side-chains 759 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 668 time to evaluate : 4.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 31 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 239 TRP Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 187 THR Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 80 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 317 LYS Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 206 PHE Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain O residue 145 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 131 LYS Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 92 LYS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 557 optimal weight: 3.9990 chunk 379 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 498 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 570 optimal weight: 6.9990 chunk 462 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 341 optimal weight: 0.9980 chunk 600 optimal weight: 7.9990 chunk 168 optimal weight: 0.1980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 179 GLN 1 305 ASN ** 4 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 208 HIS 8 83 ASN 8 199 GLN 8 229 ASN B 134 HIS B 266 GLN ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 GLN O 204 ASN R 277 ASN S 47 GLN S 91 ASN S 107 GLN U 186 ASN ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 70822 Z= 0.327 Angle : 0.791 50.506 99567 Z= 0.473 Chirality : 0.124 6.396 11638 Planarity : 0.004 0.078 9784 Dihedral : 19.414 170.002 19022 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.25 % Allowed : 12.14 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.11), residues: 6167 helix: 1.49 (0.10), residues: 2937 sheet: 0.57 (0.20), residues: 630 loop : 0.22 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 299 HIS 0.009 0.001 HIS 7 52 PHE 0.023 0.002 PHE 7 43 TYR 0.019 0.002 TYR V 91 ARG 0.007 0.000 ARG a 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 691 time to evaluate : 4.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8743 (mp) REVERT: 0 192 ASN cc_start: 0.8841 (t0) cc_final: 0.8503 (t0) REVERT: 1 268 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: 1 288 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6454 (mt-10) REVERT: 4 67 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7967 (mtmm) REVERT: 4 427 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6821 (ttm-80) REVERT: 4 507 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: 4 650 MET cc_start: 0.3739 (OUTLIER) cc_final: 0.3360 (mpm) REVERT: 5 96 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5979 (mtp) REVERT: 7 241 TYR cc_start: 0.7303 (t80) cc_final: 0.7087 (t80) REVERT: 8 100 TYR cc_start: 0.7288 (p90) cc_final: 0.6943 (p90) REVERT: 8 319 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7640 (tm130) REVERT: C 19 ARG cc_start: 0.5014 (mmt-90) cc_final: 0.4241 (tpt-90) REVERT: D 330 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8408 (mmtp) REVERT: E 50 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7449 (ttm-80) REVERT: F 138 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: F 179 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6963 (ptt90) REVERT: G 245 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7024 (tpt90) REVERT: G 267 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6468 (mtp) REVERT: G 314 MET cc_start: 0.8534 (ttp) cc_final: 0.8089 (ttp) REVERT: J 36 MET cc_start: 0.9199 (mtp) cc_final: 0.8761 (mtp) REVERT: O 62 GLU cc_start: 0.6723 (tp30) cc_final: 0.6345 (tp30) REVERT: O 65 GLN cc_start: 0.8171 (tp40) cc_final: 0.7881 (tp40) REVERT: O 145 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8443 (ttpt) REVERT: O 210 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: O 235 MET cc_start: 0.8859 (tpp) cc_final: 0.8499 (tpt) REVERT: P 87 PHE cc_start: 0.7275 (m-80) cc_final: 0.7020 (m-80) REVERT: R 72 ASP cc_start: 0.7104 (t70) cc_final: 0.6818 (t0) REVERT: R 112 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: R 127 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8089 (tttt) REVERT: R 331 PHE cc_start: 0.7846 (t80) cc_final: 0.7598 (t80) REVERT: T 9 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8609 (tp) REVERT: U 80 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7678 (ttp-110) REVERT: V 358 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6408 (mm-40) REVERT: V 396 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6441 (tm-30) REVERT: V 398 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5895 (mt-10) REVERT: W 109 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: Y 351 MET cc_start: 0.7132 (mmm) cc_final: 0.6805 (mmm) REVERT: Z 32 LYS cc_start: 0.7285 (mmmm) cc_final: 0.7069 (tppt) REVERT: Z 63 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.6067 (tp40) REVERT: a 266 MET cc_start: 0.3695 (mmm) cc_final: 0.3402 (mmm) REVERT: a 301 HIS cc_start: 0.5874 (m90) cc_final: 0.5460 (m90) outliers start: 177 outliers final: 95 residues processed: 796 average time/residue: 1.6725 time to fit residues: 1700.1356 Evaluate side-chains 785 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 665 time to evaluate : 4.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 194 GLN Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 187 THR Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 427 ARG Chi-restraints excluded: chain 4 residue 452 GLN Chi-restraints excluded: chain 4 residue 464 LEU Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 4 residue 598 LEU Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 80 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 107 ILE Chi-restraints excluded: chain 5 residue 170 THR Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 5 residue 326 LEU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 317 LYS Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 180 GLU Chi-restraints excluded: chain 8 residue 206 PHE Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain 8 residue 319 GLN Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain O residue 145 LYS Chi-restraints excluded: chain O residue 210 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain S residue 57 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 63 GLN Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain a residue 211 THR Chi-restraints excluded: chain a residue 259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 225 optimal weight: 8.9990 chunk 602 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 392 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 669 optimal weight: 5.9990 chunk 555 optimal weight: 4.9990 chunk 309 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 221 optimal weight: 10.0000 chunk 351 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 179 GLN 4 189 ASN 5 192 GLN 5 208 HIS 8 83 ASN ** 8 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN B 266 GLN F 147 GLN G 318 HIS O 204 ASN R 277 ASN S 47 GLN S 91 ASN S 107 GLN U 186 ASN W 173 GLN ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 70822 Z= 0.256 Angle : 0.755 50.558 99567 Z= 0.458 Chirality : 0.122 6.347 11638 Planarity : 0.004 0.070 9784 Dihedral : 19.335 173.123 19022 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.50 % Allowed : 13.46 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.11), residues: 6167 helix: 1.75 (0.10), residues: 2922 sheet: 0.60 (0.20), residues: 630 loop : 0.32 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 299 HIS 0.008 0.001 HIS 7 52 PHE 0.028 0.001 PHE 4 173 TYR 0.019 0.001 TYR a 322 ARG 0.011 0.000 ARG a 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 697 time to evaluate : 5.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8650 (mp) REVERT: 0 192 ASN cc_start: 0.8813 (t0) cc_final: 0.8464 (t0) REVERT: 1 268 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7683 (mt0) REVERT: 1 288 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6470 (mt-10) REVERT: 3 174 ARG cc_start: 0.8659 (ttt90) cc_final: 0.8389 (ttt90) REVERT: 4 172 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6302 (ttt) REVERT: 4 200 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.6063 (t0) REVERT: 4 507 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: 4 650 MET cc_start: 0.3708 (ptm) cc_final: 0.3494 (mpm) REVERT: 5 96 MET cc_start: 0.6247 (OUTLIER) cc_final: 0.5938 (mtp) REVERT: 7 241 TYR cc_start: 0.7247 (t80) cc_final: 0.7001 (t80) REVERT: B 181 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8318 (tp) REVERT: C 19 ARG cc_start: 0.5035 (mmt-90) cc_final: 0.4244 (tpt-90) REVERT: D 330 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8411 (mmtp) REVERT: G 245 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7013 (tpt90) REVERT: G 314 MET cc_start: 0.8510 (ttp) cc_final: 0.8041 (ttp) REVERT: J 36 MET cc_start: 0.9168 (mtp) cc_final: 0.8746 (mtp) REVERT: O 62 GLU cc_start: 0.6689 (tp30) cc_final: 0.6412 (tp30) REVERT: O 92 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8444 (mttm) REVERT: O 235 MET cc_start: 0.8862 (tpp) cc_final: 0.8490 (tpt) REVERT: P 87 PHE cc_start: 0.7266 (m-80) cc_final: 0.7019 (m-80) REVERT: R 72 ASP cc_start: 0.7053 (t70) cc_final: 0.6797 (t0) REVERT: R 112 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: R 116 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7316 (ttp-110) REVERT: R 127 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8034 (tttt) REVERT: R 315 GLN cc_start: 0.5959 (mm-40) cc_final: 0.5416 (mm110) REVERT: R 331 PHE cc_start: 0.7815 (t80) cc_final: 0.7600 (t80) REVERT: R 344 LEU cc_start: 0.7735 (tt) cc_final: 0.7488 (tt) REVERT: T 9 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8595 (tp) REVERT: T 132 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7538 (tpp-160) REVERT: U 80 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7677 (ttp-110) REVERT: V 358 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6303 (mm-40) REVERT: V 396 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6410 (tm-30) REVERT: Y 351 MET cc_start: 0.7124 (mmm) cc_final: 0.6731 (mmm) REVERT: Z 21 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6220 (mm-30) REVERT: a 266 MET cc_start: 0.3738 (mmm) cc_final: 0.3300 (mmm) outliers start: 136 outliers final: 64 residues processed: 779 average time/residue: 1.6692 time to fit residues: 1666.8016 Evaluate side-chains 747 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 666 time to evaluate : 4.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 194 GLN Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 239 TRP Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 172 MET Chi-restraints excluded: chain 4 residue 187 THR Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 317 LYS Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain S residue 57 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 645 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 381 optimal weight: 0.9990 chunk 488 optimal weight: 5.9990 chunk 378 optimal weight: 0.8980 chunk 563 optimal weight: 4.9990 chunk 373 optimal weight: 0.8980 chunk 666 optimal weight: 2.9990 chunk 417 optimal weight: 0.6980 chunk 406 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 179 GLN 4 189 ASN 5 208 HIS 8 83 ASN ** 8 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 319 GLN B 266 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 HIS O 65 GLN O 204 ASN R 277 ASN S 47 GLN S 91 ASN S 107 GLN U 117 HIS Y 296 ASN ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 70822 Z= 0.266 Angle : 0.756 50.530 99567 Z= 0.458 Chirality : 0.122 6.349 11638 Planarity : 0.004 0.080 9784 Dihedral : 19.261 175.131 19022 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.41 % Allowed : 13.94 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.11), residues: 6167 helix: 1.77 (0.10), residues: 2928 sheet: 0.67 (0.20), residues: 628 loop : 0.37 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP a 299 HIS 0.008 0.001 HIS 7 52 PHE 0.025 0.001 PHE 7 43 TYR 0.017 0.001 TYR V 91 ARG 0.007 0.000 ARG a 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 678 time to evaluate : 5.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8667 (mp) REVERT: 0 192 ASN cc_start: 0.8807 (t0) cc_final: 0.8448 (t0) REVERT: 1 268 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7658 (mt0) REVERT: 3 174 ARG cc_start: 0.8638 (ttt90) cc_final: 0.8384 (ttt90) REVERT: 4 172 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6501 (ttt) REVERT: 4 200 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.6022 (t0) REVERT: 4 507 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6060 (mp0) REVERT: 5 96 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5947 (mtp) REVERT: 7 241 TYR cc_start: 0.7244 (t80) cc_final: 0.6974 (t80) REVERT: B 181 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8321 (tp) REVERT: C 19 ARG cc_start: 0.5018 (mmt-90) cc_final: 0.4260 (tpt-90) REVERT: F 138 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: F 179 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6934 (ptt90) REVERT: G 245 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7013 (tpt90) REVERT: G 256 LEU cc_start: 0.7092 (pp) cc_final: 0.6692 (pt) REVERT: G 314 MET cc_start: 0.8536 (ttp) cc_final: 0.8086 (ttp) REVERT: J 36 MET cc_start: 0.9177 (mtp) cc_final: 0.8743 (mtp) REVERT: O 62 GLU cc_start: 0.6728 (tp30) cc_final: 0.6425 (tp30) REVERT: O 65 GLN cc_start: 0.8209 (tp40) cc_final: 0.7885 (tp40) REVERT: O 92 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8460 (mttm) REVERT: O 235 MET cc_start: 0.8849 (tpp) cc_final: 0.8477 (tpt) REVERT: P 87 PHE cc_start: 0.7278 (m-80) cc_final: 0.7024 (m-80) REVERT: R 72 ASP cc_start: 0.7045 (t70) cc_final: 0.6799 (t0) REVERT: R 112 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: R 116 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7309 (ttp-110) REVERT: R 127 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8012 (tttt) REVERT: R 315 GLN cc_start: 0.6024 (mm-40) cc_final: 0.5514 (mm110) REVERT: R 331 PHE cc_start: 0.7840 (t80) cc_final: 0.7611 (t80) REVERT: T 66 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8110 (mpp) REVERT: T 132 ARG cc_start: 0.7810 (mmt-90) cc_final: 0.7481 (tpt170) REVERT: U 36 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8244 (mptt) REVERT: U 80 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7680 (ttp-110) REVERT: V 358 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6372 (mm-40) REVERT: V 396 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6418 (tm-30) REVERT: V 398 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.5836 (mt-10) REVERT: Y 351 MET cc_start: 0.7128 (mmm) cc_final: 0.6756 (mmm) REVERT: Z 21 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6204 (mm-30) REVERT: Z 32 LYS cc_start: 0.7370 (mmmm) cc_final: 0.7108 (tppt) REVERT: a 266 MET cc_start: 0.3682 (mmm) cc_final: 0.3234 (mmm) outliers start: 131 outliers final: 69 residues processed: 754 average time/residue: 1.7086 time to fit residues: 1653.7351 Evaluate side-chains 753 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 665 time to evaluate : 5.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 31 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 194 GLN Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 172 MET Chi-restraints excluded: chain 4 residue 187 THR Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 598 LEU Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 317 LYS Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain 8 residue 319 GLN Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain S residue 57 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain U residue 36 LYS Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 412 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 chunk 398 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 424 optimal weight: 7.9990 chunk 454 optimal weight: 0.2980 chunk 329 optimal weight: 5.9990 chunk 62 optimal weight: 0.0030 chunk 524 optimal weight: 2.9990 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 179 GLN 4 189 ASN ** 5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 208 HIS 8 83 ASN 8 319 GLN B 266 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN O 204 ASN R 277 ASN S 47 GLN S 91 ASN S 107 GLN T 14 GLN T 18 GLN U 186 ASN ** Y 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 301 HIS ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 70822 Z= 0.271 Angle : 0.759 50.517 99567 Z= 0.459 Chirality : 0.122 6.353 11638 Planarity : 0.004 0.075 9784 Dihedral : 19.220 175.845 19022 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.37 % Allowed : 14.20 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.11), residues: 6167 helix: 1.77 (0.10), residues: 2926 sheet: 0.67 (0.20), residues: 630 loop : 0.38 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP a 299 HIS 0.009 0.001 HIS 7 52 PHE 0.027 0.001 PHE 7 43 TYR 0.016 0.001 TYR V 91 ARG 0.005 0.000 ARG X 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 666 time to evaluate : 4.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8663 (mp) REVERT: 0 192 ASN cc_start: 0.8802 (t0) cc_final: 0.8445 (t0) REVERT: 1 268 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: 3 174 ARG cc_start: 0.8640 (ttt90) cc_final: 0.8395 (ttt90) REVERT: 4 67 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7934 (mtmm) REVERT: 4 172 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6369 (ttt) REVERT: 4 200 ASP cc_start: 0.6509 (OUTLIER) cc_final: 0.6084 (t0) REVERT: 4 507 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: 4 650 MET cc_start: 0.4134 (OUTLIER) cc_final: 0.3340 (ptp) REVERT: 5 96 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5952 (mtp) REVERT: 7 241 TYR cc_start: 0.7190 (t80) cc_final: 0.6917 (t80) REVERT: B 181 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8322 (tp) REVERT: C 19 ARG cc_start: 0.4973 (mmt-90) cc_final: 0.4080 (tpp-160) REVERT: E 100 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6829 (mp10) REVERT: F 138 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: F 179 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6947 (ptt90) REVERT: G 245 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7025 (tpt90) REVERT: G 256 LEU cc_start: 0.7137 (pp) cc_final: 0.6738 (pt) REVERT: G 314 MET cc_start: 0.8536 (ttp) cc_final: 0.8081 (ttp) REVERT: J 36 MET cc_start: 0.9174 (mtp) cc_final: 0.8740 (mtp) REVERT: M 13 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7388 (ttt-90) REVERT: O 62 GLU cc_start: 0.6753 (tp30) cc_final: 0.6454 (tp30) REVERT: O 92 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8446 (mttm) REVERT: O 235 MET cc_start: 0.8828 (tpp) cc_final: 0.8485 (tpt) REVERT: P 87 PHE cc_start: 0.7284 (m-80) cc_final: 0.7029 (m-80) REVERT: R 72 ASP cc_start: 0.7041 (t70) cc_final: 0.6801 (t0) REVERT: R 112 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: R 116 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7318 (ttp-110) REVERT: R 127 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8018 (tttt) REVERT: R 315 GLN cc_start: 0.5912 (mm-40) cc_final: 0.5520 (mm110) REVERT: R 331 PHE cc_start: 0.7839 (t80) cc_final: 0.7636 (t80) REVERT: R 344 LEU cc_start: 0.7730 (tt) cc_final: 0.7464 (tt) REVERT: T 132 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7471 (tpt170) REVERT: U 36 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8261 (mptt) REVERT: U 80 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7662 (ttp-110) REVERT: V 358 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6409 (mm-40) REVERT: V 396 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: W 109 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: Z 21 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6188 (mm-30) REVERT: Z 65 LEU cc_start: 0.7009 (mp) cc_final: 0.6751 (mt) REVERT: a 266 MET cc_start: 0.3499 (mmm) cc_final: 0.3050 (mmm) REVERT: a 267 ARG cc_start: 0.4889 (OUTLIER) cc_final: 0.4047 (ppt170) REVERT: a 301 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.5438 (m170) outliers start: 129 outliers final: 77 residues processed: 741 average time/residue: 1.6252 time to fit residues: 1543.9965 Evaluate side-chains 753 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 652 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 194 GLN Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 172 MET Chi-restraints excluded: chain 4 residue 187 THR Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 501 ASP Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 598 LEU Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 317 LYS Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 238 ILE Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain S residue 57 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 36 LYS Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Chi-restraints excluded: chain a residue 267 ARG Chi-restraints excluded: chain a residue 301 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 606 optimal weight: 0.6980 chunk 638 optimal weight: 5.9990 chunk 582 optimal weight: 7.9990 chunk 621 optimal weight: 1.9990 chunk 374 optimal weight: 0.5980 chunk 270 optimal weight: 10.0000 chunk 488 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 561 optimal weight: 9.9990 chunk 587 optimal weight: 0.9990 chunk 619 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 179 GLN 4 189 ASN ** 5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 208 HIS 8 83 ASN 8 270 HIS B 266 GLN G 127 HIS O 65 GLN O 204 ASN R 277 ASN S 47 GLN S 91 ASN S 107 GLN T 14 GLN T 20 ASN Y 296 ASN ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 70822 Z= 0.262 Angle : 0.756 50.517 99567 Z= 0.457 Chirality : 0.122 6.342 11638 Planarity : 0.004 0.103 9784 Dihedral : 19.175 176.820 19022 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.28 % Allowed : 14.31 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.11), residues: 6167 helix: 1.80 (0.10), residues: 2924 sheet: 0.69 (0.20), residues: 634 loop : 0.40 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 375 HIS 0.010 0.001 HIS 7 52 PHE 0.037 0.001 PHE a 302 TYR 0.028 0.001 TYR a 322 ARG 0.006 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 670 time to evaluate : 5.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8656 (mp) REVERT: 0 192 ASN cc_start: 0.8806 (t0) cc_final: 0.8449 (t0) REVERT: 3 174 ARG cc_start: 0.8629 (ttt90) cc_final: 0.8393 (ttt90) REVERT: 4 67 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7927 (mtmm) REVERT: 4 172 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6411 (ttt) REVERT: 4 200 ASP cc_start: 0.6494 (OUTLIER) cc_final: 0.6085 (t0) REVERT: 4 507 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: 4 650 MET cc_start: 0.3963 (OUTLIER) cc_final: 0.3383 (ptp) REVERT: 5 96 MET cc_start: 0.6214 (OUTLIER) cc_final: 0.5907 (mtp) REVERT: 7 241 TYR cc_start: 0.7177 (t80) cc_final: 0.6941 (t80) REVERT: B 181 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8320 (tp) REVERT: C 19 ARG cc_start: 0.4972 (mmt-90) cc_final: 0.4218 (tpp-160) REVERT: E 100 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6864 (mp10) REVERT: F 138 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: F 179 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6936 (ptt90) REVERT: G 245 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7015 (tpt90) REVERT: G 256 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6791 (pt) REVERT: G 314 MET cc_start: 0.8527 (ttp) cc_final: 0.8051 (ttp) REVERT: J 36 MET cc_start: 0.9170 (mtp) cc_final: 0.8736 (mtp) REVERT: M 13 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7389 (ttt-90) REVERT: O 62 GLU cc_start: 0.6701 (tp30) cc_final: 0.6417 (tp30) REVERT: O 65 GLN cc_start: 0.8158 (tp40) cc_final: 0.7926 (tp40) REVERT: O 92 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8458 (mttm) REVERT: P 87 PHE cc_start: 0.7287 (m-80) cc_final: 0.7027 (m-80) REVERT: R 72 ASP cc_start: 0.7065 (t70) cc_final: 0.6840 (t0) REVERT: R 112 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: R 116 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7341 (ttp-110) REVERT: R 127 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8001 (tttt) REVERT: R 315 GLN cc_start: 0.5888 (mm-40) cc_final: 0.5517 (mm110) REVERT: R 331 PHE cc_start: 0.7877 (t80) cc_final: 0.7674 (t80) REVERT: R 344 LEU cc_start: 0.7702 (tt) cc_final: 0.7417 (tt) REVERT: T 20 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7905 (p0) REVERT: T 132 ARG cc_start: 0.7756 (mmt-90) cc_final: 0.7452 (tpt170) REVERT: U 36 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8248 (mptt) REVERT: U 80 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7662 (ttp-110) REVERT: V 358 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6373 (mm-40) REVERT: V 396 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6411 (tm-30) REVERT: V 398 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5823 (mt-10) REVERT: W 109 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: Z 21 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6222 (mm-30) REVERT: Z 65 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6696 (mt) REVERT: a 205 ASP cc_start: 0.5217 (t0) cc_final: 0.5005 (t70) REVERT: a 266 MET cc_start: 0.3455 (mmm) cc_final: 0.3146 (mmm) REVERT: a 267 ARG cc_start: 0.4889 (OUTLIER) cc_final: 0.4102 (ppt170) outliers start: 124 outliers final: 75 residues processed: 741 average time/residue: 1.6419 time to fit residues: 1560.2312 Evaluate side-chains 755 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 654 time to evaluate : 4.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 31 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 194 GLN Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 172 MET Chi-restraints excluded: chain 4 residue 187 THR Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 317 LYS Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 238 ILE Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain S residue 57 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 36 LYS Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 211 THR Chi-restraints excluded: chain a residue 267 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 408 optimal weight: 3.9990 chunk 657 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 456 optimal weight: 3.9990 chunk 689 optimal weight: 8.9990 chunk 634 optimal weight: 0.0470 chunk 548 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 chunk 424 optimal weight: 10.0000 chunk 336 optimal weight: 4.9990 overall best weight: 1.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 107 GLN 0 179 GLN ** 4 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 208 HIS 8 83 ASN 8 229 ASN B 266 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS O 204 ASN R 277 ASN S 47 GLN S 91 ASN S 107 GLN T 14 GLN U 186 ASN W 173 GLN a 301 HIS ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 70822 Z= 0.289 Angle : 0.770 50.516 99567 Z= 0.463 Chirality : 0.123 6.363 11638 Planarity : 0.004 0.097 9784 Dihedral : 19.164 176.730 19022 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.19 % Allowed : 14.49 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.11), residues: 6167 helix: 1.72 (0.10), residues: 2935 sheet: 0.69 (0.20), residues: 630 loop : 0.35 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 299 HIS 0.011 0.001 HIS 7 52 PHE 0.033 0.001 PHE 7 43 TYR 0.018 0.001 TYR V 91 ARG 0.006 0.000 ARG L 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 664 time to evaluate : 4.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8688 (mp) REVERT: 0 192 ASN cc_start: 0.8875 (t0) cc_final: 0.8493 (t0) REVERT: 3 174 ARG cc_start: 0.8633 (ttt90) cc_final: 0.8396 (ttt90) REVERT: 4 67 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7986 (mtmm) REVERT: 4 172 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6407 (ttt) REVERT: 4 200 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.6169 (t0) REVERT: 4 507 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6097 (mp0) REVERT: 4 599 PHE cc_start: 0.5099 (OUTLIER) cc_final: 0.4777 (m-80) REVERT: 4 650 MET cc_start: 0.3918 (OUTLIER) cc_final: 0.3393 (ptp) REVERT: 5 96 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5958 (mtp) REVERT: 7 241 TYR cc_start: 0.7216 (t80) cc_final: 0.6923 (t80) REVERT: B 181 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8341 (tp) REVERT: C 19 ARG cc_start: 0.4944 (mmt-90) cc_final: 0.4134 (tpp-160) REVERT: E 100 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: F 138 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6854 (tm-30) REVERT: F 179 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6991 (ptt90) REVERT: G 245 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7013 (tpt90) REVERT: G 256 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6860 (pt) REVERT: G 314 MET cc_start: 0.8546 (ttp) cc_final: 0.8095 (ttp) REVERT: J 36 MET cc_start: 0.9175 (mtp) cc_final: 0.8739 (mtp) REVERT: M 13 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7403 (ttt-90) REVERT: O 62 GLU cc_start: 0.6733 (tp30) cc_final: 0.6455 (tp30) REVERT: O 235 MET cc_start: 0.8845 (tpp) cc_final: 0.8487 (tpt) REVERT: P 87 PHE cc_start: 0.7299 (m-80) cc_final: 0.7032 (m-80) REVERT: R 72 ASP cc_start: 0.7067 (t70) cc_final: 0.6832 (t0) REVERT: R 112 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: R 116 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7347 (ttp-110) REVERT: R 127 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8019 (tttt) REVERT: R 315 GLN cc_start: 0.5886 (mm-40) cc_final: 0.5535 (mm110) REVERT: S 50 ARG cc_start: 0.7314 (mtt180) cc_final: 0.7016 (mmt180) REVERT: T 132 ARG cc_start: 0.7770 (mmt-90) cc_final: 0.7468 (tpt170) REVERT: U 36 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8253 (mptt) REVERT: U 80 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7662 (ttp-110) REVERT: V 358 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6404 (mm-40) REVERT: V 396 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6425 (tm-30) REVERT: V 398 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5833 (mt-10) REVERT: W 109 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: Z 21 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6224 (mm-30) REVERT: Z 32 LYS cc_start: 0.7282 (mmmm) cc_final: 0.6854 (tppt) REVERT: Z 65 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6707 (mt) REVERT: a 267 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.4045 (ppt170) REVERT: a 301 HIS cc_start: 0.5657 (OUTLIER) cc_final: 0.5343 (m170) outliers start: 119 outliers final: 73 residues processed: 732 average time/residue: 1.6266 time to fit residues: 1526.4331 Evaluate side-chains 752 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 653 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 31 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 194 GLN Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 172 MET Chi-restraints excluded: chain 4 residue 187 THR Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 452 GLN Chi-restraints excluded: chain 4 residue 464 LEU Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 599 PHE Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 317 LYS Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain S residue 57 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain U residue 36 LYS Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 267 ARG Chi-restraints excluded: chain a residue 301 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 436 optimal weight: 0.9980 chunk 584 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 506 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 549 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 564 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 107 GLN 0 179 GLN ** 4 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 208 HIS 8 83 ASN B 265 GLN B 266 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 HIS O 65 GLN O 204 ASN R 277 ASN S 47 GLN S 91 ASN S 107 GLN T 14 GLN T 20 ASN W 173 GLN a 301 HIS ** a 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.151354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116590 restraints weight = 95673.122| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.44 r_work: 0.3332 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 70822 Z= 0.298 Angle : 0.775 50.501 99567 Z= 0.465 Chirality : 0.123 6.365 11638 Planarity : 0.004 0.096 9784 Dihedral : 19.165 176.323 19022 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.11 % Allowed : 14.71 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.11), residues: 6167 helix: 1.68 (0.10), residues: 2933 sheet: 0.69 (0.20), residues: 630 loop : 0.33 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP a 299 HIS 0.014 0.001 HIS 7 52 PHE 0.037 0.001 PHE 7 43 TYR 0.033 0.001 TYR a 226 ARG 0.006 0.000 ARG L 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25285.19 seconds wall clock time: 438 minutes 44.55 seconds (26324.55 seconds total)