Starting phenix.real_space_refine (version: dev) on Tue May 17 21:35:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/05_2022/6gej_4395_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/05_2022/6gej_4395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/05_2022/6gej_4395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/05_2022/6gej_4395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/05_2022/6gej_4395_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/05_2022/6gej_4395_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "M ARG 693": "NH1" <-> "NH2" Residue "M ARG 697": "NH1" <-> "NH2" Residue "M TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 766": "NH1" <-> "NH2" Residue "M PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 787": "NH1" <-> "NH2" Residue "M ARG 815": "NH1" <-> "NH2" Residue "M ARG 833": "NH1" <-> "NH2" Residue "M ARG 926": "NH1" <-> "NH2" Residue "M ARG 956": "NH1" <-> "NH2" Residue "M TYR 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 967": "NH1" <-> "NH2" Residue "M PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1023": "NH1" <-> "NH2" Residue "M PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1133": "NH1" <-> "NH2" Residue "M ASP 1178": "OD1" <-> "OD2" Residue "M ARG 1291": "NH1" <-> "NH2" Residue "M ARG 1313": "NH1" <-> "NH2" Residue "M ARG 1357": "NH1" <-> "NH2" Residue "M TYR 1367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1387": "NH1" <-> "NH2" Residue "R PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 221": "NH1" <-> "NH2" Residue "R ARG 234": "NH1" <-> "NH2" Residue "R PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 288": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 276": "NH1" <-> "NH2" Residue "T ARG 23": "NH1" <-> "NH2" Residue "T PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 126": "NH1" <-> "NH2" Residue "T TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 223": "OD1" <-> "OD2" Residue "T ARG 258": "NH1" <-> "NH2" Residue "T ARG 348": "NH1" <-> "NH2" Residue "T ASP 378": "OD1" <-> "OD2" Residue "T ARG 392": "NH1" <-> "NH2" Residue "U ARG 52": "NH1" <-> "NH2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "U PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 122": "NH1" <-> "NH2" Residue "U TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 182": "OE1" <-> "OE2" Residue "U ARG 204": "NH1" <-> "NH2" Residue "U PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 266": "NH1" <-> "NH2" Residue "U ARG 333": "NH1" <-> "NH2" Residue "U ARG 397": "NH1" <-> "NH2" Residue "U ARG 413": "NH1" <-> "NH2" Residue "U ARG 425": "NH1" <-> "NH2" Residue "U ARG 435": "NH1" <-> "NH2" Residue "U TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 444": "OE1" <-> "OE2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V ARG 191": "NH1" <-> "NH2" Residue "V ASP 198": "OD1" <-> "OD2" Residue "V TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 242": "OE1" <-> "OE2" Residue "V ARG 258": "NH1" <-> "NH2" Residue "V ARG 348": "NH1" <-> "NH2" Residue "V ASP 365": "OD1" <-> "OD2" Residue "V ARG 392": "NH1" <-> "NH2" Residue "V ARG 413": "NH1" <-> "NH2" Residue "V TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 69": "NH1" <-> "NH2" Residue "W PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 122": "NH1" <-> "NH2" Residue "W TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 188": "OD1" <-> "OD2" Residue "W ARG 204": "NH1" <-> "NH2" Residue "W PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 228": "OE1" <-> "OE2" Residue "W PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 266": "NH1" <-> "NH2" Residue "W ARG 311": "NH1" <-> "NH2" Residue "W ARG 333": "NH1" <-> "NH2" Residue "W TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 397": "NH1" <-> "NH2" Residue "W ARG 413": "NH1" <-> "NH2" Residue "W GLU 421": "OE1" <-> "OE2" Residue "W ARG 425": "NH1" <-> "NH2" Residue "W ARG 435": "NH1" <-> "NH2" Residue "W TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X GLU 37": "OE1" <-> "OE2" Residue "X ARG 43": "NH1" <-> "NH2" Residue "X PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 126": "NH1" <-> "NH2" Residue "X ARG 132": "NH1" <-> "NH2" Residue "X TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 180": "NH1" <-> "NH2" Residue "X TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 191": "NH1" <-> "NH2" Residue "X ASP 198": "OD1" <-> "OD2" Residue "X TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 214": "NH1" <-> "NH2" Residue "X TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 221": "OE1" <-> "OE2" Residue "X TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 236": "OE1" <-> "OE2" Residue "X ARG 348": "NH1" <-> "NH2" Residue "X ASP 365": "OD1" <-> "OD2" Residue "X GLU 385": "OE1" <-> "OE2" Residue "X ARG 386": "NH1" <-> "NH2" Residue "X PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 33": "OE1" <-> "OE2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 69": "NH1" <-> "NH2" Residue "Y PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 122": "NH1" <-> "NH2" Residue "Y TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 204": "NH1" <-> "NH2" Residue "Y PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Y ASP 218": "OD1" <-> "OD2" Residue "Y PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 311": "NH1" <-> "NH2" Residue "Y ASP 315": "OD1" <-> "OD2" Residue "Y ARG 333": "NH1" <-> "NH2" Residue "Y TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 397": "NH1" <-> "NH2" Residue "Y ARG 413": "NH1" <-> "NH2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ASP 450": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 43702 Number of models: 1 Model: "" Number of chains: 29 Chain: "Z" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 655 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'TRANS': 130} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 131 Planarities with less than four sites: {'UNK:plan-1': 131} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 651 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3137 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "J" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3177 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "M" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5398 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 19, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 167 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1695 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 3 Chain: "T" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3391 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3299 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3336 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3325 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3410 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 436} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'BEF': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'BEF': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23040 SG CYS S 244 89.133 119.821 106.290 1.00 89.97 S ATOM 23060 SG CYS S 247 92.310 121.520 103.015 1.00 92.50 S ATOM 23176 SG CYS S 264 91.902 118.182 103.872 1.00 91.58 S ATOM 23201 SG CYS S 268 93.891 120.081 106.264 1.00102.36 S ATOM 23120 SG CYS S 256 87.365 114.091 115.274 1.00 92.66 S ATOM 23141 SG CYS S 259 85.271 117.144 116.015 1.00 90.81 S ATOM 23280 SG CYS S 277 87.907 117.396 119.028 1.00103.89 S Time building chain proxies: 24.10, per 1000 atoms: 0.55 Number of scatterers: 43702 At special positions: 0 Unit cell: (147.63, 197.58, 203.13, 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 2 29.99 S 118 16.00 P 324 15.00 Mg 8 11.99 F 6 9.00 O 8976 8.00 N 7737 7.00 C 26529 6.00 Be 2 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.39 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 264 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " Number of angles added : 9 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9030 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 194 helices and 33 sheets defined 44.2% alpha, 11.0% beta 151 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 15.17 Creating SS restraints... Processing helix chain 'Z' and resid 102 through 128 Processing helix chain 'Z' and resid 137 through 143 Processing helix chain 'Z' and resid 199 through 206 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.660A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.893A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.660A pdb=" N ARG B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 76 Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.894A pdb=" N ARG B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 31 through 40 Processing helix chain 'C' and resid 50 through 75 removed outlier: 3.578A pdb=" N GLU C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 31 through 40 Processing helix chain 'D' and resid 50 through 75 removed outlier: 3.578A pdb=" N GLU D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'E' and resid 18 through 21 No H-bonds generated for 'chain 'E' and resid 18 through 21' Processing helix chain 'E' and resid 28 through 37 Processing helix chain 'E' and resid 48 through 73 Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'F' and resid 18 through 21 No H-bonds generated for 'chain 'F' and resid 18 through 21' Processing helix chain 'F' and resid 28 through 37 Processing helix chain 'F' and resid 48 through 73 Processing helix chain 'F' and resid 81 through 90 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'G' and resid 41 through 51 Processing helix chain 'G' and resid 59 through 86 removed outlier: 3.511A pdb=" N GLU G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 107 through 125 Processing helix chain 'H' and resid 41 through 51 Processing helix chain 'H' and resid 59 through 86 removed outlier: 3.510A pdb=" N GLU H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 107 through 124 Processing helix chain 'M' and resid 698 through 711 removed outlier: 4.163A pdb=" N SER M 709 " --> pdb=" O ASN M 705 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU M 710 " --> pdb=" O TRP M 706 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR M 711 " --> pdb=" O LEU M 707 " (cutoff:3.500A) Processing helix chain 'M' and resid 727 through 741 removed outlier: 3.706A pdb=" N ALA M 739 " --> pdb=" O LEU M 735 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS M 740 " --> pdb=" O ALA M 736 " (cutoff:3.500A) Processing helix chain 'M' and resid 757 through 766 removed outlier: 3.919A pdb=" N GLU M 761 " --> pdb=" O LEU M 757 " (cutoff:3.500A) Processing helix chain 'M' and resid 782 through 787 Processing helix chain 'M' and resid 804 through 813 removed outlier: 3.960A pdb=" N ASP M 809 " --> pdb=" O VAL M 806 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN M 810 " --> pdb=" O VAL M 807 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N HIS M 811 " --> pdb=" O GLN M 808 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE M 813 " --> pdb=" O GLN M 810 " (cutoff:3.500A) Processing helix chain 'M' and resid 835 through 839 Processing helix chain 'M' and resid 860 through 870 Processing helix chain 'M' and resid 914 through 924 removed outlier: 3.687A pdb=" N HIS M 922 " --> pdb=" O VAL M 918 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN M 923 " --> pdb=" O ALA M 919 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL M 924 " --> pdb=" O LYS M 920 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 970 Processing helix chain 'M' and resid 972 through 974 No H-bonds generated for 'chain 'M' and resid 972 through 974' Processing helix chain 'M' and resid 979 through 993 removed outlier: 3.683A pdb=" N VAL M 983 " --> pdb=" O PHE M 979 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN M 988 " --> pdb=" O ASN M 984 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU M 989 " --> pdb=" O CYS M 985 " (cutoff:3.500A) Processing helix chain 'M' and resid 1014 through 1029 removed outlier: 3.597A pdb=" N TYR M1018 " --> pdb=" O VAL M1014 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP M1020 " --> pdb=" O SER M1016 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL M1021 " --> pdb=" O ASP M1017 " (cutoff:3.500A) Processing helix chain 'M' and resid 1047 through 1049 No H-bonds generated for 'chain 'M' and resid 1047 through 1049' Processing helix chain 'M' and resid 1057 through 1064 Processing helix chain 'M' and resid 1070 through 1093 removed outlier: 3.585A pdb=" N LEU M1078 " --> pdb=" O GLU M1074 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU M1080 " --> pdb=" O ASN M1076 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU M1085 " --> pdb=" O THR M1081 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU M1088 " --> pdb=" O GLN M1084 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU M1091 " --> pdb=" O GLU M1087 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ALA M1092 " --> pdb=" O GLU M1088 " (cutoff:3.500A) Processing helix chain 'M' and resid 1104 through 1133 removed outlier: 3.623A pdb=" N ASN M1108 " --> pdb=" O PHE M1104 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP M1117 " --> pdb=" O GLU M1113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET M1118 " --> pdb=" O GLY M1114 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU M1122 " --> pdb=" O MET M1118 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS M1123 " --> pdb=" O LEU M1119 " (cutoff:3.500A) Processing helix chain 'M' and resid 1142 through 1146 Processing helix chain 'M' and resid 1158 through 1163 removed outlier: 3.787A pdb=" N ILE M1163 " --> pdb=" O ASN M1160 " (cutoff:3.500A) Processing helix chain 'M' and resid 1166 through 1172 removed outlier: 3.800A pdb=" N LEU M1171 " --> pdb=" O GLN M1167 " (cutoff:3.500A) Processing helix chain 'M' and resid 1174 through 1180 Processing helix chain 'M' and resid 1192 through 1197 Processing helix chain 'M' and resid 1207 through 1219 removed outlier: 3.794A pdb=" N LEU M1211 " --> pdb=" O GLU M1207 " (cutoff:3.500A) Processing helix chain 'M' and resid 1223 through 1232 removed outlier: 4.175A pdb=" N GLN M1226 " --> pdb=" O PRO M1223 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M1230 " --> pdb=" O LEU M1227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR M1232 " --> pdb=" O THR M1229 " (cutoff:3.500A) Processing helix chain 'M' and resid 1240 through 1243 No H-bonds generated for 'chain 'M' and resid 1240 through 1243' Processing helix chain 'M' and resid 1251 through 1260 Processing helix chain 'M' and resid 1272 through 1285 removed outlier: 4.305A pdb=" N ASP M1276 " --> pdb=" O LYS M1273 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU M1282 " --> pdb=" O GLU M1279 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN M1283 " --> pdb=" O GLN M1280 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS M1285 " --> pdb=" O LEU M1282 " (cutoff:3.500A) Processing helix chain 'M' and resid 1299 through 1309 removed outlier: 4.019A pdb=" N ILE M1303 " --> pdb=" O GLU M1299 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE M1308 " --> pdb=" O LEU M1304 " (cutoff:3.500A) Processing helix chain 'M' and resid 1349 through 1355 removed outlier: 3.832A pdb=" N CYS M1355 " --> pdb=" O CYS M1351 " (cutoff:3.500A) Processing helix chain 'M' and resid 1375 through 1385 removed outlier: 3.656A pdb=" N LEU M1380 " --> pdb=" O GLU M1376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS M1381 " --> pdb=" O SER M1377 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN M1385 " --> pdb=" O LYS M1381 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 48 No H-bonds generated for 'chain 'R' and resid 46 through 48' Processing helix chain 'R' and resid 69 through 81 Processing helix chain 'R' and resid 109 through 121 Processing helix chain 'R' and resid 133 through 142 removed outlier: 3.654A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) Proline residue: R 138 - end of helix removed outlier: 4.980A pdb=" N LYS R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 133 through 142' Processing helix chain 'R' and resid 220 through 234 Processing helix chain 'R' and resid 242 through 252 Processing helix chain 'R' and resid 260 through 265 Processing helix chain 'R' and resid 308 through 316 Proline residue: R 314 - end of helix Processing helix chain 'R' and resid 320 through 323 Processing helix chain 'R' and resid 330 through 339 Processing helix chain 'R' and resid 343 through 349 Proline residue: R 347 - end of helix No H-bonds generated for 'chain 'R' and resid 343 through 349' Processing helix chain 'R' and resid 359 through 361 No H-bonds generated for 'chain 'R' and resid 359 through 361' Processing helix chain 'R' and resid 365 through 376 removed outlier: 3.854A pdb=" N GLN R 376 " --> pdb=" O GLU R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 405 removed outlier: 3.896A pdb=" N ALA R 404 " --> pdb=" O MET R 400 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 412 removed outlier: 3.995A pdb=" N LYS R 411 " --> pdb=" O ASP R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing helix chain 'R' and resid 424 through 429 removed outlier: 3.970A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 60 Processing helix chain 'S' and resid 92 through 106 Processing helix chain 'S' and resid 113 through 124 Proline residue: S 117 - end of helix Processing helix chain 'S' and resid 128 through 134 Processing helix chain 'S' and resid 169 through 181 removed outlier: 4.495A pdb=" N SER S 181 " --> pdb=" O LEU S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 202 Processing helix chain 'S' and resid 208 through 213 Processing helix chain 'S' and resid 219 through 225 Processing helix chain 'S' and resid 266 through 272 Processing helix chain 'T' and resid 52 through 67 removed outlier: 3.522A pdb=" N VAL T 60 " --> pdb=" O GLU T 56 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE T 61 " --> pdb=" O ALA T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 96 removed outlier: 3.781A pdb=" N SER T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 109 No H-bonds generated for 'chain 'T' and resid 107 through 109' Processing helix chain 'T' and resid 117 through 128 Processing helix chain 'T' and resid 183 through 192 Processing helix chain 'T' and resid 217 through 221 removed outlier: 3.994A pdb=" N THR T 220 " --> pdb=" O ALA T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 257 Processing helix chain 'T' and resid 265 through 272 Processing helix chain 'T' and resid 282 through 298 removed outlier: 3.555A pdb=" N ASP T 297 " --> pdb=" O ALA T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 313 through 315 No H-bonds generated for 'chain 'T' and resid 313 through 315' Processing helix chain 'T' and resid 318 through 328 removed outlier: 3.640A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 358 No H-bonds generated for 'chain 'T' and resid 356 through 358' Processing helix chain 'T' and resid 361 through 366 removed outlier: 3.724A pdb=" N ARG T 366 " --> pdb=" O ASP T 362 " (cutoff:3.500A) Processing helix chain 'T' and resid 377 through 391 Processing helix chain 'T' and resid 397 through 409 removed outlier: 3.602A pdb=" N LEU T 402 " --> pdb=" O SER T 398 " (cutoff:3.500A) Processing helix chain 'T' and resid 412 through 428 removed outlier: 3.713A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix removed outlier: 4.192A pdb=" N ILE T 424 " --> pdb=" O ALA T 420 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 445 removed outlier: 3.974A pdb=" N LEU T 444 " --> pdb=" O ASN T 440 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU T 445 " --> pdb=" O GLU T 441 " (cutoff:3.500A) Processing helix chain 'T' and resid 449 through 457 Processing helix chain 'U' and resid 48 through 63 Processing helix chain 'U' and resid 82 through 92 Processing helix chain 'U' and resid 113 through 123 removed outlier: 3.800A pdb=" N ALA U 120 " --> pdb=" O ALA U 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE U 121 " --> pdb=" O LEU U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 181 Processing helix chain 'U' and resid 241 through 249 removed outlier: 3.694A pdb=" N ILE U 247 " --> pdb=" O GLU U 243 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN U 248 " --> pdb=" O ILE U 244 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER U 249 " --> pdb=" O ASP U 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 254 through 259 removed outlier: 3.556A pdb=" N PHE U 258 " --> pdb=" O PHE U 254 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 283 removed outlier: 3.722A pdb=" N THR U 275 " --> pdb=" O ASP U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 300 No H-bonds generated for 'chain 'U' and resid 298 through 300' Processing helix chain 'U' and resid 303 through 313 removed outlier: 3.618A pdb=" N ASN U 310 " --> pdb=" O PHE U 306 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 342 No H-bonds generated for 'chain 'U' and resid 340 through 342' Processing helix chain 'U' and resid 345 through 350 removed outlier: 3.823A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 361 through 374 removed outlier: 3.694A pdb=" N LYS U 365 " --> pdb=" O GLU U 361 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR U 366 " --> pdb=" O GLN U 362 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 393 Processing helix chain 'U' and resid 396 through 412 removed outlier: 4.361A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 443 removed outlier: 3.642A pdb=" N GLU U 442 " --> pdb=" O LYS U 438 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 85 through 96 removed outlier: 3.591A pdb=" N ALA V 91 " --> pdb=" O ALA V 87 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER V 93 " --> pdb=" O ALA V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 110 removed outlier: 3.666A pdb=" N LEU V 110 " --> pdb=" O GLY V 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 107 through 110' Processing helix chain 'V' and resid 117 through 127 removed outlier: 3.742A pdb=" N ASN V 124 " --> pdb=" O THR V 120 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE V 125 " --> pdb=" O LEU V 121 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG V 126 " --> pdb=" O MET V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 192 Processing helix chain 'V' and resid 216 through 218 No H-bonds generated for 'chain 'V' and resid 216 through 218' Processing helix chain 'V' and resid 249 through 257 removed outlier: 3.581A pdb=" N ALA V 255 " --> pdb=" O ASP V 251 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN V 256 " --> pdb=" O LEU V 252 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 273 Processing helix chain 'V' and resid 282 through 297 Processing helix chain 'V' and resid 313 through 315 No H-bonds generated for 'chain 'V' and resid 313 through 315' Processing helix chain 'V' and resid 318 through 327 removed outlier: 3.738A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 358 No H-bonds generated for 'chain 'V' and resid 356 through 358' Processing helix chain 'V' and resid 361 through 365 removed outlier: 3.690A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 361 through 365' Processing helix chain 'V' and resid 377 through 390 Processing helix chain 'V' and resid 397 through 409 Processing helix chain 'V' and resid 412 through 428 removed outlier: 3.821A pdb=" N LEU V 419 " --> pdb=" O ALA V 415 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA V 420 " --> pdb=" O LEU V 416 " (cutoff:3.500A) Proline residue: V 421 - end of helix Processing helix chain 'V' and resid 436 through 445 Processing helix chain 'V' and resid 449 through 457 Processing helix chain 'W' and resid 48 through 63 removed outlier: 3.517A pdb=" N ILE W 57 " --> pdb=" O ALA W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 92 Processing helix chain 'W' and resid 113 through 124 removed outlier: 3.974A pdb=" N SER W 124 " --> pdb=" O ALA W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 173 through 181 removed outlier: 3.862A pdb=" N ASP W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 247 Processing helix chain 'W' and resid 252 through 259 removed outlier: 4.100A pdb=" N THR W 259 " --> pdb=" O ALA W 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 283 removed outlier: 3.525A pdb=" N THR W 275 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 303 through 314 removed outlier: 3.872A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU W 314 " --> pdb=" O ASN W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 342 No H-bonds generated for 'chain 'W' and resid 340 through 342' Processing helix chain 'W' and resid 345 through 350 removed outlier: 3.992A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 361 through 375 removed outlier: 3.508A pdb=" N LYS W 365 " --> pdb=" O GLU W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 381 through 393 Processing helix chain 'W' and resid 396 through 411 removed outlier: 3.585A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN W 407 " --> pdb=" O ILE W 403 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN W 408 " --> pdb=" O SER W 404 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 429 Processing helix chain 'W' and resid 433 through 442 removed outlier: 3.712A pdb=" N LYS W 438 " --> pdb=" O ALA W 434 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR W 439 " --> pdb=" O ARG W 435 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 85 through 96 removed outlier: 3.736A pdb=" N ALA X 89 " --> pdb=" O LYS X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 110 removed outlier: 3.558A pdb=" N LEU X 110 " --> pdb=" O GLY X 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 107 through 110' Processing helix chain 'X' and resid 117 through 126 Processing helix chain 'X' and resid 183 through 192 removed outlier: 3.592A pdb=" N GLU X 187 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE X 189 " --> pdb=" O TYR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 218 No H-bonds generated for 'chain 'X' and resid 216 through 218' Processing helix chain 'X' and resid 249 through 257 removed outlier: 3.582A pdb=" N ALA X 255 " --> pdb=" O ASP X 251 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 270 Processing helix chain 'X' and resid 282 through 297 Processing helix chain 'X' and resid 313 through 315 No H-bonds generated for 'chain 'X' and resid 313 through 315' Processing helix chain 'X' and resid 318 through 327 removed outlier: 3.575A pdb=" N ASN X 325 " --> pdb=" O PHE X 321 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 361 through 366 removed outlier: 3.951A pdb=" N ARG X 366 " --> pdb=" O ASP X 362 " (cutoff:3.500A) Processing helix chain 'X' and resid 377 through 391 removed outlier: 3.848A pdb=" N THR X 389 " --> pdb=" O GLU X 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL X 390 " --> pdb=" O ARG X 386 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 409 removed outlier: 3.686A pdb=" N LEU X 402 " --> pdb=" O SER X 398 " (cutoff:3.500A) Processing helix chain 'X' and resid 412 through 428 removed outlier: 3.745A pdb=" N LEU X 419 " --> pdb=" O ALA X 415 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA X 420 " --> pdb=" O LEU X 416 " (cutoff:3.500A) Proline residue: X 421 - end of helix Processing helix chain 'X' and resid 436 through 445 Processing helix chain 'X' and resid 449 through 457 removed outlier: 3.772A pdb=" N GLU X 457 " --> pdb=" O THR X 453 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 63 removed outlier: 3.674A pdb=" N ILE Y 57 " --> pdb=" O ALA Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 92 Processing helix chain 'Y' and resid 103 through 106 removed outlier: 3.738A pdb=" N ILE Y 106 " --> pdb=" O GLY Y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 103 through 106' Processing helix chain 'Y' and resid 113 through 122 Processing helix chain 'Y' and resid 173 through 180 Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 267 through 283 removed outlier: 3.838A pdb=" N ASP Y 271 " --> pdb=" O SER Y 267 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN Y 272 " --> pdb=" O GLU Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 303 through 314 removed outlier: 4.702A pdb=" N GLU Y 314 " --> pdb=" O ASN Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 342 No H-bonds generated for 'chain 'Y' and resid 340 through 342' Processing helix chain 'Y' and resid 345 through 349 Processing helix chain 'Y' and resid 361 through 375 removed outlier: 3.519A pdb=" N LYS Y 365 " --> pdb=" O GLU Y 361 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR Y 366 " --> pdb=" O GLN Y 362 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU Y 374 " --> pdb=" O ILE Y 370 " (cutoff:3.500A) Processing helix chain 'Y' and resid 383 through 393 removed outlier: 3.627A pdb=" N GLU Y 393 " --> pdb=" O LYS Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 396 through 413 removed outlier: 3.916A pdb=" N SER Y 400 " --> pdb=" O LEU Y 396 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN Y 401 " --> pdb=" O ARG Y 397 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU Y 402 " --> pdb=" O TYR Y 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN Y 407 " --> pdb=" O ILE Y 403 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 442 removed outlier: 3.757A pdb=" N VAL Y 437 " --> pdb=" O SER Y 433 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'Z' and resid 169 through 171 Processing sheet with id= B, first strand: chain 'M' and resid 719 through 721 removed outlier: 5.480A pdb=" N LEU M 930 " --> pdb=" O ALA M 720 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'M' and resid 800 through 802 removed outlier: 5.882A pdb=" N ILE M 750 " --> pdb=" O VAL M 801 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ARG M 847 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU M 823 " --> pdb=" O ARG M 847 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU M 849 " --> pdb=" O LEU M 823 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 944 through 946 removed outlier: 6.738A pdb=" N VAL M1364 " --> pdb=" O TYR M 945 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'M' and resid 949 through 951 Processing sheet with id= F, first strand: chain 'M' and resid 1335 through 1338 removed outlier: 4.077A pdb=" N THR M1269 " --> pdb=" O LEU M1319 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET M1290 " --> pdb=" O VAL M1316 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 127 through 130 removed outlier: 6.397A pdb=" N ILE R 6 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER R 102 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE R 8 " --> pdb=" O SER R 102 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'R' and resid 32 through 35 Processing sheet with id= I, first strand: chain 'R' and resid 147 through 151 Processing sheet with id= J, first strand: chain 'R' and resid 353 through 356 removed outlier: 6.431A pdb=" N LEU R 189 " --> pdb=" O VAL R 354 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR R 356 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE R 191 " --> pdb=" O THR R 356 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 286 through 289 removed outlier: 3.976A pdb=" N TYR R 286 " --> pdb=" O VAL R 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL R 275 " --> pdb=" O TYR R 286 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 369 through 372 removed outlier: 8.558A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLY T 79 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER T 340 " --> pdb=" O GLY T 79 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA T 339 " --> pdb=" O ILE T 310 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 246 through 248 Processing sheet with id= N, first strand: chain 'T' and resid 238 through 243 removed outlier: 3.713A pdb=" N GLY T 213 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'T' and resid 147 through 150 removed outlier: 3.593A pdb=" N HIS T 165 " --> pdb=" O GLU T 150 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 351 through 355 removed outlier: 7.208A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA U 324 " --> pdb=" O ILE U 295 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'U' and resid 286 through 290 removed outlier: 3.605A pdb=" N GLY U 126 " --> pdb=" O VAL U 289 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'U' and resid 166 through 170 removed outlier: 3.567A pdb=" N THR U 167 " --> pdb=" O ILE U 160 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU U 142 " --> pdb=" O THR U 159 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL U 140 " --> pdb=" O ASP U 188 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'V' and resid 367 through 371 removed outlier: 7.130A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'V' and resid 246 through 248 removed outlier: 3.536A pdb=" N LEU V 131 " --> pdb=" O VAL V 247 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG V 132 " --> pdb=" O GLU V 302 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'V' and resid 238 through 243 removed outlier: 3.740A pdb=" N LYS V 241 " --> pdb=" O LYS V 137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY V 142 " --> pdb=" O ILE V 200 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE V 200 " --> pdb=" O GLY V 142 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'V' and resid 147 through 149 removed outlier: 3.825A pdb=" N THR V 148 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE V 167 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'V' and resid 344 through 346 Processing sheet with id= X, first strand: chain 'W' and resid 351 through 354 removed outlier: 7.304A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'W' and resid 230 through 240 Processing sheet with id= Z, first strand: chain 'W' and resid 166 through 171 removed outlier: 4.273A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE W 190 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL W 140 " --> pdb=" O ASP W 188 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL W 189 " --> pdb=" O GLY W 203 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'X' and resid 367 through 371 removed outlier: 7.568A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA X 339 " --> pdb=" O ILE X 310 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'X' and resid 238 through 248 removed outlier: 3.706A pdb=" N LYS X 241 " --> pdb=" O LYS X 137 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'X' and resid 139 through 142 removed outlier: 3.912A pdb=" N GLY X 142 " --> pdb=" O ILE X 200 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY X 213 " --> pdb=" O VAL X 199 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'X' and resid 175 through 182 removed outlier: 7.010A pdb=" N GLU X 150 " --> pdb=" O SER X 164 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL X 166 " --> pdb=" O THR X 148 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR X 148 " --> pdb=" O VAL X 166 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Y' and resid 353 through 355 removed outlier: 8.530A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL Y 321 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL Y 73 " --> pdb=" O VAL Y 321 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N MET Y 323 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA Y 324 " --> pdb=" O ILE Y 295 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Y' and resid 230 through 240 removed outlier: 3.625A pdb=" N LEU Y 135 " --> pdb=" O LYS Y 231 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Y' and resid 166 through 170 removed outlier: 3.844A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP Y 188 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) 1390 hydrogen bonds defined for protein. 4020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 23.84 Time building geometry restraints manager: 18.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12690 1.34 - 1.46: 7653 1.46 - 1.57: 23823 1.57 - 1.69: 638 1.69 - 1.81: 194 Bond restraints: 44998 Sorted by residual: bond pdb=" F2 BEF R 502 " pdb="BE BEF R 502 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" F2 BEF M1602 " pdb="BE BEF M1602 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F3 BEF M1602 " pdb="BE BEF M1602 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" F3 BEF R 502 " pdb="BE BEF R 502 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" F1 BEF M1602 " pdb="BE BEF M1602 " ideal model delta sigma weight residual 1.476 1.535 -0.059 2.00e-02 2.50e+03 8.56e+00 ... (remaining 44993 not shown) Histogram of bond angle deviations from ideal: 97.54 - 105.30: 1878 105.30 - 113.06: 25796 113.06 - 120.82: 21168 120.82 - 128.59: 12975 128.59 - 136.35: 390 Bond angle restraints: 62207 Sorted by residual: angle pdb=" C LEU M 998 " pdb=" N PHE M 999 " pdb=" CA PHE M 999 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.39e+01 angle pdb=" N MET V 406 " pdb=" CA MET V 406 " pdb=" C MET V 406 " ideal model delta sigma weight residual 110.97 105.70 5.27 1.09e+00 8.42e-01 2.34e+01 angle pdb=" C LEU U 29 " pdb=" CA LEU U 29 " pdb=" CB LEU U 29 " ideal model delta sigma weight residual 116.54 111.05 5.49 1.15e+00 7.56e-01 2.28e+01 angle pdb=" F2 BEF M1602 " pdb="BE BEF M1602 " pdb=" F3 BEF M1602 " ideal model delta sigma weight residual 119.96 107.15 12.81 3.00e+00 1.11e-01 1.82e+01 angle pdb=" F2 BEF R 502 " pdb="BE BEF R 502 " pdb=" F3 BEF R 502 " ideal model delta sigma weight residual 119.96 107.27 12.69 3.00e+00 1.11e-01 1.79e+01 ... (remaining 62202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 24744 35.89 - 71.79: 1558 71.79 - 107.68: 34 107.68 - 143.57: 9 143.57 - 179.46: 4 Dihedral angle restraints: 26349 sinusoidal: 12398 harmonic: 13951 Sorted by residual: dihedral pdb=" CA UNK Z 188 " pdb=" C UNK Z 188 " pdb=" N UNK Z 189 " pdb=" CA UNK Z 189 " ideal model delta harmonic sigma weight residual -180.00 -139.72 -40.28 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA LEU M 692 " pdb=" C LEU M 692 " pdb=" N ARG M 693 " pdb=" CA ARG M 693 " ideal model delta harmonic sigma weight residual 180.00 -143.52 -36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" C5' ADP W 501 " pdb=" O5' ADP W 501 " pdb=" PA ADP W 501 " pdb=" O2A ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 119.47 -179.46 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 26346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 5406 0.035 - 0.069: 1316 0.069 - 0.104: 406 0.104 - 0.139: 158 0.139 - 0.173: 2 Chirality restraints: 7288 Sorted by residual: chirality pdb=" CA MET V 406 " pdb=" N MET V 406 " pdb=" C MET V 406 " pdb=" CB MET V 406 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA TYR V 462 " pdb=" N TYR V 462 " pdb=" C TYR V 462 " pdb=" CB TYR V 462 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA VAL T 359 " pdb=" N VAL T 359 " pdb=" C VAL T 359 " pdb=" CB VAL T 359 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 7285 not shown) Planarity restraints: 6836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE T 304 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO T 305 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO T 305 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO T 305 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 998 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C LEU M 998 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU M 998 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE M 999 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP V 182 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO V 183 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO V 183 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO V 183 " 0.027 5.00e-02 4.00e+02 ... (remaining 6833 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 10 2.17 - 2.85: 14055 2.85 - 3.54: 60353 3.54 - 4.22: 103596 4.22 - 4.90: 168414 Nonbonded interactions: 346428 Sorted by model distance: nonbonded pdb=" CE MET T 406 " pdb=" CD1 LEU T 418 " model vdw 1.491 3.880 nonbonded pdb=" OG1 THR Y 82 " pdb="MG MG Y 502 " model vdw 2.076 2.170 nonbonded pdb=" O1B ADP R 501 " pdb="MG MG R 503 " model vdw 2.077 2.170 nonbonded pdb=" N2 DG I -68 " pdb=" O2 DC J 68 " model vdw 2.132 2.496 nonbonded pdb=" OG1 THR U 162 " pdb=" O MET U 165 " model vdw 2.140 2.440 ... (remaining 346423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 23 through 102) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 17 through 117) selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 35 through 125) selection = chain 'H' } ncs_group { reference = (chain 'T' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 463 or resid 501)) selection = (chain 'V' and (resid 22 through 161 or (resid 162 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) selection = (chain 'X' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 161 through 163 and (name N or name CA or \ name C or name O or name CB )) or resid 164 through 463 or resid 501)) } ncs_group { reference = (chain 'U' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 222 or (resid 223 and (name N or name C \ A or name C or name O or name CB )) or resid 224 through 459)) selection = (chain 'W' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 205 or resid 222 throug \ h 459)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 205 or resid 222 or (resid 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 through 45 \ 9)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 324 5.49 5 Mg 8 5.21 5 S 118 5.16 5 Be 2 3.05 5 C 26529 2.51 5 N 7737 2.21 5 O 8976 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.040 Extract box with map and model: 15.320 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.390 Process input model: 131.770 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.003 0.086 44998 Z= 0.153 Angle : 0.621 12.807 62207 Z= 0.365 Chirality : 0.037 0.173 7288 Planarity : 0.003 0.056 6836 Dihedral : 18.571 179.465 17319 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.10), residues: 4633 helix: -2.29 (0.08), residues: 2159 sheet: -0.39 (0.18), residues: 655 loop : -1.42 (0.12), residues: 1819 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 966 time to evaluate : 4.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 35 residues processed: 1091 average time/residue: 0.6070 time to fit residues: 1038.6392 Evaluate side-chains 424 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 389 time to evaluate : 4.589 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4158 time to fit residues: 32.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 426 optimal weight: 3.9990 chunk 382 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 258 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 395 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 240 optimal weight: 1.9990 chunk 294 optimal weight: 0.8980 chunk 458 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 GLN E 74 ASN F 39 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS H 112 HIS M 716 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 857 GLN M 940 GLN M1058 HIS M1226 GLN M1283 ASN M1302 GLN ** M1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 HIS R 98 HIS R 251 GLN R 374 GLN S 176 GLN T 256 ASN T 271 GLN U 119 GLN U 252 GLN U 451 GLN V 27 HIS V 124 ASN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 63 ASN W 455 GLN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 238 HIS X 256 ASN ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN Y 144 GLN Y 223 GLN Y 272 GLN Y 451 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 44998 Z= 0.209 Angle : 0.641 11.545 62207 Z= 0.328 Chirality : 0.041 0.231 7288 Planarity : 0.005 0.106 6836 Dihedral : 22.804 156.679 8363 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.74 % Favored : 97.24 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.11), residues: 4633 helix: -0.66 (0.10), residues: 2177 sheet: 0.09 (0.18), residues: 682 loop : -1.29 (0.13), residues: 1774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 429 time to evaluate : 4.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 68 residues processed: 533 average time/residue: 0.5614 time to fit residues: 493.2550 Evaluate side-chains 376 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 308 time to evaluate : 4.661 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.4033 time to fit residues: 56.7439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 254 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 381 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 459 optimal weight: 2.9990 chunk 496 optimal weight: 2.9990 chunk 409 optimal weight: 0.8980 chunk 455 optimal weight: 0.0670 chunk 156 optimal weight: 0.9990 chunk 368 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 ASN F 42 GLN G 98 GLN M 712 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 155 GLN V 124 ASN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 44998 Z= 0.183 Angle : 0.597 12.636 62207 Z= 0.305 Chirality : 0.040 0.230 7288 Planarity : 0.004 0.127 6836 Dihedral : 22.676 152.161 8363 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.37 % Favored : 96.61 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 4633 helix: 0.12 (0.11), residues: 2174 sheet: 0.14 (0.18), residues: 680 loop : -1.15 (0.13), residues: 1779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 364 time to evaluate : 4.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 36 residues processed: 446 average time/residue: 0.5597 time to fit residues: 417.0617 Evaluate side-chains 340 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 4.559 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3904 time to fit residues: 32.9791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 453 optimal weight: 4.9990 chunk 345 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 219 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 461 optimal weight: 1.9990 chunk 488 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 436 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 GLN E 74 ASN F 42 GLN M 712 ASN ** M 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 811 HIS ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1285 HIS ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 367 GLN S 97 GLN U 25 HIS V 124 ASN V 263 GLN ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 357 HIS W 63 ASN W 230 GLN W 299 HIS X 271 GLN ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.101 44998 Z= 0.452 Angle : 0.790 14.256 62207 Z= 0.408 Chirality : 0.046 0.220 7288 Planarity : 0.006 0.131 6836 Dihedral : 22.854 154.917 8363 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.66 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 4633 helix: -0.08 (0.11), residues: 2161 sheet: -0.36 (0.19), residues: 690 loop : -1.36 (0.13), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 317 time to evaluate : 4.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 83 residues processed: 446 average time/residue: 0.5644 time to fit residues: 417.1507 Evaluate side-chains 364 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 281 time to evaluate : 4.302 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 0.4060 time to fit residues: 68.7737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 406 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 363 optimal weight: 0.0670 chunk 201 optimal weight: 2.9990 chunk 416 optimal weight: 4.9990 chunk 337 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 249 optimal weight: 1.9990 chunk 438 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1356 HIS R 319 HIS ** V 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN ** W 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 GLN Y 299 HIS ** Y 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.142 44998 Z= 0.253 Angle : 0.646 12.738 62207 Z= 0.331 Chirality : 0.041 0.273 7288 Planarity : 0.004 0.141 6836 Dihedral : 22.764 155.033 8363 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.92 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 4633 helix: 0.33 (0.11), residues: 2143 sheet: -0.26 (0.19), residues: 672 loop : -1.27 (0.13), residues: 1818 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 321 time to evaluate : 5.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 38 residues processed: 382 average time/residue: 0.5805 time to fit residues: 365.1012 Evaluate side-chains 318 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 280 time to evaluate : 4.630 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4095 time to fit residues: 34.7430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 164 optimal weight: 2.9990 chunk 439 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 488 optimal weight: 7.9990 chunk 405 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 256 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN M 712 ASN ** M 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 744 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 HIS V 124 ASN V 205 ASN ** W 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.108 44998 Z= 0.360 Angle : 0.695 10.521 62207 Z= 0.357 Chirality : 0.043 0.216 7288 Planarity : 0.005 0.133 6836 Dihedral : 22.775 156.426 8363 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.12), residues: 4633 helix: 0.23 (0.11), residues: 2164 sheet: -0.46 (0.19), residues: 675 loop : -1.36 (0.14), residues: 1794 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 304 time to evaluate : 4.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 45 residues processed: 371 average time/residue: 0.5865 time to fit residues: 361.1192 Evaluate side-chains 326 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 281 time to evaluate : 4.408 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4450 time to fit residues: 42.8325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 471 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 356 optimal weight: 0.8980 chunk 276 optimal weight: 0.6980 chunk 411 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 chunk 486 optimal weight: 0.8980 chunk 304 optimal weight: 0.0030 chunk 296 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN ** M 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 759 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 997 ASN R 422 HIS ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 23 HIS W 272 GLN ** Y 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.145 44998 Z= 0.189 Angle : 0.616 14.317 62207 Z= 0.315 Chirality : 0.040 0.214 7288 Planarity : 0.004 0.133 6836 Dihedral : 22.663 155.838 8363 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.96 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.12), residues: 4633 helix: 0.64 (0.11), residues: 2142 sheet: -0.28 (0.20), residues: 667 loop : -1.17 (0.14), residues: 1824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 318 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 356 average time/residue: 0.5662 time to fit residues: 333.3930 Evaluate side-chains 300 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 278 time to evaluate : 4.643 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.3857 time to fit residues: 22.2016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 301 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 309 optimal weight: 0.7980 chunk 331 optimal weight: 6.9990 chunk 240 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 382 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 GLN ** X 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.148 44998 Z= 0.405 Angle : 0.737 13.445 62207 Z= 0.380 Chirality : 0.044 0.227 7288 Planarity : 0.006 0.139 6836 Dihedral : 22.768 157.866 8363 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.30 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.12), residues: 4633 helix: 0.30 (0.11), residues: 2149 sheet: -0.56 (0.19), residues: 673 loop : -1.37 (0.14), residues: 1811 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 280 time to evaluate : 4.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 35 residues processed: 320 average time/residue: 0.5600 time to fit residues: 298.8299 Evaluate side-chains 299 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 4.677 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3969 time to fit residues: 32.1252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 442 optimal weight: 5.9990 chunk 466 optimal weight: 0.4980 chunk 425 optimal weight: 0.8980 chunk 453 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 356 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 409 optimal weight: 5.9990 chunk 428 optimal weight: 5.9990 chunk 451 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 ASN E 83 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 712 ASN ** M 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 260 GLN ** V 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 GLN X 154 ASN ** Y 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.332 44998 Z= 0.245 Angle : 0.644 23.314 62207 Z= 0.333 Chirality : 0.040 0.198 7288 Planarity : 0.004 0.131 6836 Dihedral : 22.710 157.136 8363 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.42 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4633 helix: 0.62 (0.11), residues: 2134 sheet: -0.44 (0.20), residues: 671 loop : -1.25 (0.14), residues: 1828 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 288 time to evaluate : 4.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 299 average time/residue: 0.5597 time to fit residues: 280.2577 Evaluate side-chains 275 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 271 time to evaluate : 4.512 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4297 time to fit residues: 9.1527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 297 optimal weight: 1.9990 chunk 479 optimal weight: 0.2980 chunk 292 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 333 optimal weight: 0.0970 chunk 503 optimal weight: 1.9990 chunk 463 optimal weight: 4.9990 chunk 400 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 155 GLN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN ** Y 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.152 44998 Z= 0.220 Angle : 0.632 17.669 62207 Z= 0.325 Chirality : 0.040 0.198 7288 Planarity : 0.004 0.126 6836 Dihedral : 22.632 157.483 8363 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.14 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 4633 helix: 0.72 (0.11), residues: 2147 sheet: -0.38 (0.20), residues: 667 loop : -1.21 (0.14), residues: 1819 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 290 time to evaluate : 4.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 301 average time/residue: 0.5562 time to fit residues: 282.0109 Evaluate side-chains 277 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 271 time to evaluate : 4.542 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3884 time to fit residues: 10.4370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 318 optimal weight: 20.0000 chunk 426 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 369 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 401 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 412 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 341 HIS ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.117433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.088507 restraints weight = 110057.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088347 restraints weight = 96361.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088439 restraints weight = 77603.884| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.467 44998 Z= 0.370 Angle : 0.790 73.818 62207 Z= 0.380 Chirality : 0.040 0.204 7288 Planarity : 0.005 0.204 6836 Dihedral : 22.630 157.582 8363 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4633 helix: 0.74 (0.11), residues: 2137 sheet: -0.37 (0.20), residues: 667 loop : -1.21 (0.14), residues: 1829 =============================================================================== Job complete usr+sys time: 8322.55 seconds wall clock time: 153 minutes 10.87 seconds (9190.87 seconds total)