Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 23:38:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/04_2023/8css_26969_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/04_2023/8css_26969.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/04_2023/8css_26969_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/04_2023/8css_26969_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/04_2023/8css_26969_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/04_2023/8css_26969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/04_2023/8css_26969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/04_2023/8css_26969_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/04_2023/8css_26969_neut_updated.pdb" } resolution = 2.36 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= 0.033 sd= 1.280 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 7 8.98 5 Fe 8 7.16 5 Zn 1 6.06 5 P 853 5.49 5 Mg 32 5.21 5 S 252 5.16 5 C 39455 2.51 5 N 12095 2.21 5 O 14763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 13": "OE1" <-> "OE2" Residue "0 GLU 23": "OE1" <-> "OE2" Residue "0 ASP 30": "OD1" <-> "OD2" Residue "0 GLU 148": "OE1" <-> "OE2" Residue "0 TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 177": "OE1" <-> "OE2" Residue "1 ASP 128": "OD1" <-> "OD2" Residue "1 GLU 144": "OE1" <-> "OE2" Residue "1 TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 184": "OD1" <-> "OD2" Residue "1 GLU 306": "OE1" <-> "OE2" Residue "4 TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 281": "OE1" <-> "OE2" Residue "4 GLU 366": "OE1" <-> "OE2" Residue "4 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 443": "OD1" <-> "OD2" Residue "4 PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 GLU 123": "OE1" <-> "OE2" Residue "6 ASP 132": "OD1" <-> "OD2" Residue "6 GLU 192": "OE1" <-> "OE2" Residue "7 ASP 38": "OD1" <-> "OD2" Residue "7 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 308": "OD1" <-> "OD2" Residue "7 ASP 311": "OD1" <-> "OD2" Residue "7 GLU 318": "OE1" <-> "OE2" Residue "7 ASP 407": "OD1" <-> "OD2" Residue "8 GLU 133": "OE1" <-> "OE2" Residue "8 PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 170": "OE1" <-> "OE2" Residue "8 TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 187": "OE1" <-> "OE2" Residue "8 PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 243": "OE1" <-> "OE2" Residue "8 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D ASP 394": "OD1" <-> "OD2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 217": "OD1" <-> "OD2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "G GLU 358": "OE1" <-> "OE2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L GLU 126": "OE1" <-> "OE2" Residue "M PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "O ASP 197": "OD1" <-> "OD2" Residue "P ASP 73": "OD1" <-> "OD2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 67": "OE1" <-> "OE2" Residue "R ASP 282": "OD1" <-> "OD2" Residue "R ASP 292": "OD1" <-> "OD2" Residue "R ASP 295": "OD1" <-> "OD2" Residue "R TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 43": "OE1" <-> "OE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "T TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 138": "OE1" <-> "OE2" Residue "T TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 92": "OE1" <-> "OE2" Residue "U GLU 101": "OE1" <-> "OE2" Residue "U GLU 171": "OE1" <-> "OE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 278": "OE1" <-> "OE2" Residue "V ASP 281": "OD1" <-> "OD2" Residue "V GLU 315": "OE1" <-> "OE2" Residue "V GLU 370": "OE1" <-> "OE2" Residue "V TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W ASP 111": "OD1" <-> "OD2" Residue "W ASP 159": "OD1" <-> "OD2" Residue "X GLU 53": "OE1" <-> "OE2" Residue "X ASP 74": "OD1" <-> "OD2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X ASP 149": "OD1" <-> "OD2" Residue "X PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 217": "OE1" <-> "OE2" Residue "X GLU 286": "OE1" <-> "OE2" Residue "X GLU 327": "OE1" <-> "OE2" Residue "X GLU 332": "OE1" <-> "OE2" Residue "X PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 362": "OE1" <-> "OE2" Residue "Y ASP 279": "OD1" <-> "OD2" Residue "Y GLU 312": "OE1" <-> "OE2" Residue "Y GLU 318": "OE1" <-> "OE2" Residue "Y GLU 327": "OE1" <-> "OE2" Residue "Y PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 67466 Number of models: 1 Model: "" Number of chains: 44 Chain: "0" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1754 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "1" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2098 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Chain: "3" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 625 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4585 Classifications: {'peptide': 566} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 3 Chain: "6" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Chain: "7" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3160 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 368} Chain breaks: 1 Chain: "8" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2543 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain: "A" Number of atoms: 17959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 17959 Classifications: {'RNA': 846} Modifications used: {'rna2p_pur': 64, 'rna2p_pyr': 65, 'rna3p': 2, 'rna3p_pur': 372, 'rna3p_pyr': 343} Link IDs: {'rna2p': 128, 'rna3p': 717} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1789 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "C" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1042 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1838 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 858 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "F" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1696 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain: "G" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2395 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain breaks: 1 Chain: "H" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1064 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 8, 'TRANS': 121} Chain breaks: 1 Chain: "I" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1019 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "J" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 97} Chain: "K" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 323 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain breaks: 1 Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1363 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "M" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 913 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1570 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 21, 'TRANS': 168} Chain: "P" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "Q" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 744 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2382 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain: "S" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1100 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "T" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "U" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1468 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "V" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2946 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 9, 'TRANS': 349} Chain breaks: 1 Chain: "W" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "X" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2849 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 332} Chain: "Y" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1043 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "Z" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain breaks: 1 Chain: "7" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 81 Unusual residues: {' K': 7, ' MG': 30, 'NAD': 1} Classifications: {'undetermined': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12924 SG CYS 7 404 95.731 111.461 158.486 1.00 24.52 S ATOM 12445 SG CYS 7 347 98.809 107.183 154.129 1.00 19.22 S ATOM 12340 SG CYS 7 333 92.598 109.386 153.498 1.00 22.66 S ATOM 12387 SG CYS 7 339 97.841 112.680 152.559 1.00 22.91 S ATOM 50123 SG CYS O 94 113.628 164.038 95.464 1.00 28.93 S ATOM 50209 SG CYS O 105 116.367 164.541 93.211 1.00 27.66 S ATOM 50230 SG CYS O 108 115.378 167.523 94.956 1.00 30.79 S ATOM 50518 SG CYS O 143 113.014 166.047 92.204 1.00 24.24 S ATOM 51441 SG CYS P 65 123.290 74.762 52.060 1.00 47.18 S ATOM 51714 SG CYS P 100 120.427 77.389 52.867 1.00 42.47 S ATOM 39217 SG CYS E 105 123.189 80.172 48.942 1.00 66.52 S ATOM 51463 SG CYS P 68 124.514 76.499 47.987 1.00 48.82 S ATOM 48068 SG CYS M 26 92.077 175.277 73.581 1.00 28.94 S ATOM 57504 SG CYS T 149 95.434 175.266 74.505 1.00 32.10 S ATOM 57432 SG CYS T 139 94.552 176.268 68.090 1.00 29.83 S ATOM 57446 SG CYS T 141 97.460 176.215 70.720 1.00 30.12 S Time building chain proxies: 26.41, per 1000 atoms: 0.39 Number of scatterers: 67466 At special positions: 0 Unit cell: (225.144, 245.322, 215.586, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 8 26.01 K 7 19.00 S 252 16.00 P 853 15.00 Mg 32 11.99 O 14763 8.00 N 12095 7.00 C 39455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.18 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 201 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 100 " pdb="FE2 FES P 201 " - pdb=" SG CYS E 105 " pdb="FE2 FES P 201 " - pdb=" SG CYS P 68 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 65 " pdb=" FES T 201 " pdb="FE1 FES T 201 " - pdb=" SG CYS T 149 " pdb="FE1 FES T 201 " - pdb=" SG CYS M 26 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 141 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 139 " pdb=" SF4 7 501 " pdb="FE4 SF4 7 501 " - pdb=" SG CYS 7 339 " pdb="FE2 SF4 7 501 " - pdb=" SG CYS 7 347 " pdb="FE3 SF4 7 501 " - pdb=" SG CYS 7 333 " pdb="FE1 SF4 7 501 " - pdb=" SG CYS 7 404 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 105 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 108 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 143 " Number of angles added : 6 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 258 helices and 37 sheets defined 47.1% alpha, 9.1% beta 236 base pairs and 411 stacking pairs defined. Time for finding SS restraints: 21.89 Creating SS restraints... Processing helix chain '0' and resid 10 through 25 Processing helix chain '0' and resid 30 through 33 No H-bonds generated for 'chain '0' and resid 30 through 33' Processing helix chain '0' and resid 52 through 59 removed outlier: 5.048A pdb=" N ALA 0 56 " --> pdb=" O ARG 0 53 " (cutoff:3.500A) Processing helix chain '0' and resid 64 through 70 removed outlier: 4.557A pdb=" N ARG 0 70 " --> pdb=" O GLN 0 66 " (cutoff:3.500A) Processing helix chain '0' and resid 72 through 75 Processing helix chain '0' and resid 83 through 88 Processing helix chain '0' and resid 144 through 151 removed outlier: 5.379A pdb=" N GLU 0 148 " --> pdb=" O HIS 0 145 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR 0 151 " --> pdb=" O GLU 0 148 " (cutoff:3.500A) Processing helix chain '0' and resid 168 through 180 Processing helix chain '0' and resid 207 through 209 No H-bonds generated for 'chain '0' and resid 207 through 209' Processing helix chain '1' and resid 56 through 59 Processing helix chain '1' and resid 66 through 69 No H-bonds generated for 'chain '1' and resid 66 through 69' Processing helix chain '1' and resid 103 through 106 No H-bonds generated for 'chain '1' and resid 103 through 106' Processing helix chain '1' and resid 116 through 129 removed outlier: 3.753A pdb=" N ALA 1 125 " --> pdb=" O LYS 1 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS 1 127 " --> pdb=" O CYS 1 123 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP 1 128 " --> pdb=" O GLU 1 124 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE 1 129 " --> pdb=" O ALA 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 146 Processing helix chain '1' and resid 166 through 169 removed outlier: 3.912A pdb=" N ARG 1 169 " --> pdb=" O PRO 1 166 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 166 through 169' Processing helix chain '1' and resid 177 through 179 No H-bonds generated for 'chain '1' and resid 177 through 179' Processing helix chain '1' and resid 184 through 197 removed outlier: 6.611A pdb=" N GLU 1 196 " --> pdb=" O LYS 1 192 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG 1 197 " --> pdb=" O LEU 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 215 through 233 Processing helix chain '1' and resid 239 through 241 No H-bonds generated for 'chain '1' and resid 239 through 241' Processing helix chain '1' and resid 257 through 272 Processing helix chain '1' and resid 287 through 301 Processing helix chain '1' and resid 306 through 320 Processing helix chain '3' and resid 130 through 149 Processing helix chain '3' and resid 151 through 180 Processing helix chain '4' and resid 69 through 77 Processing helix chain '4' and resid 100 through 123 Processing helix chain '4' and resid 125 through 127 No H-bonds generated for 'chain '4' and resid 125 through 127' Processing helix chain '4' and resid 138 through 140 No H-bonds generated for 'chain '4' and resid 138 through 140' Processing helix chain '4' and resid 154 through 163 Processing helix chain '4' and resid 166 through 179 Processing helix chain '4' and resid 185 through 198 Processing helix chain '4' and resid 243 through 250 Processing helix chain '4' and resid 256 through 268 Processing helix chain '4' and resid 272 through 284 Processing helix chain '4' and resid 291 through 303 Processing helix chain '4' and resid 309 through 325 Processing helix chain '4' and resid 332 through 362 removed outlier: 4.305A pdb=" N ARG 4 344 " --> pdb=" O LYS 4 340 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE 4 345 " --> pdb=" O CYS 4 341 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N HIS 4 346 " --> pdb=" O LEU 4 342 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL 4 347 " --> pdb=" O ARG 4 343 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE 4 348 " --> pdb=" O ARG 4 344 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA 4 349 " --> pdb=" O PHE 4 345 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG 4 350 " --> pdb=" O HIS 4 346 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N SER 4 351 " --> pdb=" O VAL 4 347 " (cutoff:3.500A) Proline residue: 4 352 - end of helix Processing helix chain '4' and resid 369 through 379 Processing helix chain '4' and resid 391 through 400 Processing helix chain '4' and resid 410 through 426 removed outlier: 4.338A pdb=" N ASP 4 413 " --> pdb=" O PRO 4 410 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE 4 416 " --> pdb=" O ASP 4 413 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN 4 417 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU 4 426 " --> pdb=" O CYS 4 423 " (cutoff:3.500A) Processing helix chain '4' and resid 429 through 439 Processing helix chain '4' and resid 444 through 448 Processing helix chain '4' and resid 451 through 468 Processing helix chain '4' and resid 471 through 481 Processing helix chain '4' and resid 490 through 503 Processing helix chain '4' and resid 506 through 518 Proline residue: 4 510 - end of helix Processing helix chain '4' and resid 521 through 523 No H-bonds generated for 'chain '4' and resid 521 through 523' Processing helix chain '4' and resid 525 through 536 Processing helix chain '4' and resid 542 through 560 Processing helix chain '4' and resid 573 through 586 Processing helix chain '4' and resid 589 through 602 removed outlier: 4.030A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) Processing helix chain '4' and resid 608 through 620 Processing helix chain '4' and resid 624 through 637 removed outlier: 3.532A pdb=" N PHE 4 637 " --> pdb=" O LEU 4 633 " (cutoff:3.500A) Processing helix chain '4' and resid 640 through 652 removed outlier: 3.775A pdb=" N GLU 4 643 " --> pdb=" O PRO 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 657 through 666 Processing helix chain '6' and resid 44 through 49 Processing helix chain '6' and resid 91 through 108 Processing helix chain '6' and resid 115 through 120 Processing helix chain '6' and resid 146 through 169 removed outlier: 5.145A pdb=" N ALA 6 161 " --> pdb=" O GLN 6 157 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N HIS 6 162 " --> pdb=" O ARG 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 186 through 197 removed outlier: 3.601A pdb=" N LEU 6 190 " --> pdb=" O GLY 6 186 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 46 No H-bonds generated for 'chain '7' and resid 43 through 46' Processing helix chain '7' and resid 65 through 74 Processing helix chain '7' and resid 81 through 96 removed outlier: 3.741A pdb=" N ASN 7 85 " --> pdb=" O PRO 7 81 " (cutoff:3.500A) Processing helix chain '7' and resid 103 through 116 removed outlier: 3.525A pdb=" N ARG 7 108 " --> pdb=" O GLU 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 133 through 139 Processing helix chain '7' and resid 152 through 180 removed outlier: 6.266A pdb=" N ASP 7 164 " --> pdb=" O ALA 7 160 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY 7 165 " --> pdb=" O ALA 7 161 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 198 through 207 removed outlier: 3.513A pdb=" N ILE 7 206 " --> pdb=" O ALA 7 202 " (cutoff:3.500A) Processing helix chain '7' and resid 221 through 232 Processing helix chain '7' and resid 268 through 270 No H-bonds generated for 'chain '7' and resid 268 through 270' Processing helix chain '7' and resid 274 through 286 Processing helix chain '7' and resid 300 through 314 Processing helix chain '7' and resid 417 through 420 No H-bonds generated for 'chain '7' and resid 417 through 420' Processing helix chain '7' and resid 422 through 430 Processing helix chain '8' and resid 87 through 98 Processing helix chain '8' and resid 102 through 107 Processing helix chain '8' and resid 112 through 115 No H-bonds generated for 'chain '8' and resid 112 through 115' Processing helix chain '8' and resid 117 through 138 removed outlier: 3.819A pdb=" N GLN 8 121 " --> pdb=" O THR 8 117 " (cutoff:3.500A) Proline residue: 8 122 - end of helix Processing helix chain '8' and resid 140 through 144 Processing helix chain '8' and resid 155 through 162 Processing helix chain '8' and resid 168 through 188 Processing helix chain '8' and resid 204 through 218 removed outlier: 3.572A pdb=" N CYS 8 215 " --> pdb=" O ALA 8 211 " (cutoff:3.500A) Processing helix chain '8' and resid 242 through 250 Processing helix chain '8' and resid 252 through 255 No H-bonds generated for 'chain '8' and resid 252 through 255' Processing helix chain '8' and resid 272 through 287 Proline residue: 8 276 - end of helix removed outlier: 4.126A pdb=" N GLU 8 279 " --> pdb=" O PRO 8 276 " (cutoff:3.500A) Proline residue: 8 280 - end of helix removed outlier: 3.807A pdb=" N ALA 8 287 " --> pdb=" O ALA 8 284 " (cutoff:3.500A) Processing helix chain '8' and resid 309 through 321 removed outlier: 4.320A pdb=" N HIS 8 313 " --> pdb=" O GLY 8 310 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS 8 314 " --> pdb=" O HIS 8 311 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU 8 316 " --> pdb=" O HIS 8 313 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN 8 319 " --> pdb=" O LEU 8 316 " (cutoff:3.500A) Processing helix chain '8' and resid 326 through 334 Processing helix chain '8' and resid 353 through 361 Processing helix chain '8' and resid 363 through 368 removed outlier: 4.135A pdb=" N SER 8 368 " --> pdb=" O GLN 8 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 100 through 105 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 118 through 137 removed outlier: 3.539A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 161 removed outlier: 3.574A pdb=" N SER B 152 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR B 153 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 243 through 273 Processing helix chain 'C' and resid 21 through 24 No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 53 through 56 No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 129 through 147 Processing helix chain 'D' and resid 264 through 277 removed outlier: 3.803A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 318 through 327 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 408 through 415 Processing helix chain 'E' and resid 15 through 31 Processing helix chain 'E' and resid 72 through 84 removed outlier: 4.639A pdb=" N GLU E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 51 No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 60 through 71 removed outlier: 3.689A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 104 through 127 Processing helix chain 'F' and resid 133 through 136 removed outlier: 3.586A pdb=" N THR F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 133 through 136' Processing helix chain 'F' and resid 141 through 152 removed outlier: 3.531A pdb=" N CYS F 152 " --> pdb=" O ALA F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 191 Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.658A pdb=" N HIS F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 231 Processing helix chain 'F' and resid 234 through 239 removed outlier: 3.636A pdb=" N ALA F 237 " --> pdb=" O ARG F 234 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS F 238 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 92 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 111 Processing helix chain 'G' and resid 119 through 121 No H-bonds generated for 'chain 'G' and resid 119 through 121' Processing helix chain 'G' and resid 128 through 131 No H-bonds generated for 'chain 'G' and resid 128 through 131' Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 156 through 174 Processing helix chain 'G' and resid 202 through 209 Processing helix chain 'G' and resid 215 through 230 Processing helix chain 'G' and resid 235 through 244 removed outlier: 3.923A pdb=" N PHE G 244 " --> pdb=" O PHE G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 303 No H-bonds generated for 'chain 'G' and resid 300 through 303' Processing helix chain 'G' and resid 307 through 320 Proline residue: G 316 - end of helix removed outlier: 3.625A pdb=" N VAL G 320 " --> pdb=" O PRO G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 355 removed outlier: 4.535A pdb=" N SER G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE G 355 " --> pdb=" O ALA G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 366 Processing helix chain 'H' and resid 85 through 101 Processing helix chain 'H' and resid 150 through 162 Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'I' and resid 80 through 82 No H-bonds generated for 'chain 'I' and resid 80 through 82' Processing helix chain 'I' and resid 119 through 121 No H-bonds generated for 'chain 'I' and resid 119 through 121' Processing helix chain 'I' and resid 125 through 142 removed outlier: 4.039A pdb=" N LYS I 142 " --> pdb=" O ARG I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 167 removed outlier: 4.249A pdb=" N MET I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 39 Processing helix chain 'K' and resid 49 through 57 removed outlier: 3.766A pdb=" N ILE K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 116 removed outlier: 3.724A pdb=" N ARG K 112 " --> pdb=" O ARG K 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 82 through 84 No H-bonds generated for 'chain 'L' and resid 82 through 84' Processing helix chain 'L' and resid 87 through 92 Processing helix chain 'L' and resid 95 through 97 No H-bonds generated for 'chain 'L' and resid 95 through 97' Processing helix chain 'L' and resid 100 through 115 Processing helix chain 'L' and resid 125 through 145 removed outlier: 3.811A pdb=" N LYS L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 173 Processing helix chain 'L' and resid 175 through 185 Processing helix chain 'L' and resid 201 through 224 Processing helix chain 'M' and resid 70 through 78 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 101 through 123 Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'O' and resid 55 through 60 removed outlier: 4.047A pdb=" N LEU O 59 " --> pdb=" O PRO O 55 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU O 60 " --> pdb=" O TRP O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 60' Processing helix chain 'O' and resid 62 through 68 Processing helix chain 'O' and resid 120 through 126 removed outlier: 3.767A pdb=" N GLN O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 140 No H-bonds generated for 'chain 'O' and resid 137 through 140' Processing helix chain 'O' and resid 144 through 159 Processing helix chain 'O' and resid 191 through 195 Processing helix chain 'O' and resid 201 through 203 No H-bonds generated for 'chain 'O' and resid 201 through 203' Processing helix chain 'O' and resid 210 through 219 Processing helix chain 'P' and resid 77 through 83 removed outlier: 3.758A pdb=" N GLN P 82 " --> pdb=" O GLN P 78 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 97 No H-bonds generated for 'chain 'P' and resid 94 through 97' Processing helix chain 'P' and resid 101 through 116 Processing helix chain 'P' and resid 127 through 129 No H-bonds generated for 'chain 'P' and resid 127 through 129' Processing helix chain 'Q' and resid 19 through 32 Processing helix chain 'Q' and resid 35 through 41 Processing helix chain 'Q' and resid 48 through 78 removed outlier: 4.145A pdb=" N ARG Q 77 " --> pdb=" O ASN Q 73 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LYS Q 78 " --> pdb=" O PHE Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 83 Processing helix chain 'R' and resid 87 through 90 No H-bonds generated for 'chain 'R' and resid 87 through 90' Processing helix chain 'R' and resid 108 through 125 Processing helix chain 'R' and resid 146 through 148 No H-bonds generated for 'chain 'R' and resid 146 through 148' Processing helix chain 'R' and resid 186 through 196 Processing helix chain 'R' and resid 208 through 210 No H-bonds generated for 'chain 'R' and resid 208 through 210' Processing helix chain 'R' and resid 212 through 220 Processing helix chain 'R' and resid 224 through 234 Processing helix chain 'R' and resid 240 through 256 Processing helix chain 'R' and resid 259 through 261 No H-bonds generated for 'chain 'R' and resid 259 through 261' Processing helix chain 'R' and resid 268 through 277 Processing helix chain 'R' and resid 282 through 290 Processing helix chain 'R' and resid 294 through 307 Processing helix chain 'R' and resid 312 through 320 Processing helix chain 'R' and resid 324 through 335 removed outlier: 4.702A pdb=" N GLU R 335 " --> pdb=" O ALA R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'S' and resid 12 through 21 Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 66 through 77 removed outlier: 4.050A pdb=" N ILE S 70 " --> pdb=" O HIS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 108 Processing helix chain 'S' and resid 114 through 128 Processing helix chain 'T' and resid 8 through 11 Processing helix chain 'T' and resid 13 through 18 Processing helix chain 'T' and resid 39 through 50 removed outlier: 5.017A pdb=" N GLY T 43 " --> pdb=" O LEU T 40 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE T 50 " --> pdb=" O PHE T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 58 Processing helix chain 'T' and resid 95 through 106 Processing helix chain 'T' and resid 110 through 123 removed outlier: 3.916A pdb=" N LEU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 142 No H-bonds generated for 'chain 'T' and resid 140 through 142' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 161 through 164 No H-bonds generated for 'chain 'T' and resid 161 through 164' Processing helix chain 'U' and resid 50 through 87 Processing helix chain 'U' and resid 89 through 166 removed outlier: 3.880A pdb=" N LYS U 165 " --> pdb=" O GLN U 161 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN U 166 " --> pdb=" O GLU U 162 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 181 Processing helix chain 'V' and resid 32 through 35 No H-bonds generated for 'chain 'V' and resid 32 through 35' Processing helix chain 'V' and resid 38 through 41 No H-bonds generated for 'chain 'V' and resid 38 through 41' Processing helix chain 'V' and resid 50 through 62 Processing helix chain 'V' and resid 69 through 78 Processing helix chain 'V' and resid 82 through 96 Processing helix chain 'V' and resid 101 through 103 No H-bonds generated for 'chain 'V' and resid 101 through 103' Processing helix chain 'V' and resid 106 through 118 Processing helix chain 'V' and resid 122 through 130 Processing helix chain 'V' and resid 132 through 135 No H-bonds generated for 'chain 'V' and resid 132 through 135' Processing helix chain 'V' and resid 141 through 153 Processing helix chain 'V' and resid 157 through 170 Processing helix chain 'V' and resid 176 through 192 removed outlier: 4.065A pdb=" N LYS V 192 " --> pdb=" O HIS V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 198 through 214 Proline residue: V 211 - end of helix removed outlier: 3.851A pdb=" N LYS V 214 " --> pdb=" O LEU V 210 " (cutoff:3.500A) Processing helix chain 'V' and resid 218 through 238 Processing helix chain 'V' and resid 240 through 244 Processing helix chain 'V' and resid 255 through 267 Processing helix chain 'V' and resid 277 through 290 Processing helix chain 'V' and resid 323 through 344 Proline residue: V 328 - end of helix Processing helix chain 'V' and resid 352 through 404 removed outlier: 5.447A pdb=" N SER V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N THR V 366 " --> pdb=" O GLU V 362 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 85 Processing helix chain 'W' and resid 88 through 92 Processing helix chain 'W' and resid 131 through 133 No H-bonds generated for 'chain 'W' and resid 131 through 133' Processing helix chain 'X' and resid 56 through 58 No H-bonds generated for 'chain 'X' and resid 56 through 58' Processing helix chain 'X' and resid 61 through 63 No H-bonds generated for 'chain 'X' and resid 61 through 63' Processing helix chain 'X' and resid 72 through 78 Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.650A pdb=" N MET X 89 " --> pdb=" O PRO X 85 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN X 90 " --> pdb=" O ARG X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 113 Processing helix chain 'X' and resid 134 through 148 removed outlier: 3.671A pdb=" N GLN X 148 " --> pdb=" O PHE X 144 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 162 Processing helix chain 'X' and resid 181 through 194 removed outlier: 3.690A pdb=" N ASN X 190 " --> pdb=" O THR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 198 through 201 No H-bonds generated for 'chain 'X' and resid 198 through 201' Processing helix chain 'X' and resid 222 through 231 Processing helix chain 'X' and resid 233 through 253 removed outlier: 4.934A pdb=" N THR X 237 " --> pdb=" O ARG X 234 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP X 238 " --> pdb=" O ASN X 235 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY X 241 " --> pdb=" O ASP X 238 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE X 242 " --> pdb=" O ALA X 239 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS X 248 " --> pdb=" O LYS X 245 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN X 250 " --> pdb=" O LEU X 247 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER X 251 " --> pdb=" O LYS X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 267 No H-bonds generated for 'chain 'X' and resid 265 through 267' Processing helix chain 'X' and resid 284 through 286 No H-bonds generated for 'chain 'X' and resid 284 through 286' Processing helix chain 'X' and resid 288 through 297 removed outlier: 3.888A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET X 297 " --> pdb=" O LEU X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 337 removed outlier: 7.045A pdb=" N LYS X 331 " --> pdb=" O GLU X 327 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLU X 332 " --> pdb=" O LEU X 328 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY X 333 " --> pdb=" O LEU X 329 " (cutoff:3.500A) Processing helix chain 'X' and resid 350 through 362 Processing helix chain 'X' and resid 374 through 384 Processing helix chain 'X' and resid 388 through 397 removed outlier: 3.904A pdb=" N TYR X 397 " --> pdb=" O ARG X 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 277 through 289 removed outlier: 3.578A pdb=" N THR Y 288 " --> pdb=" O LYS Y 284 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) Processing helix chain 'Y' and resid 297 through 307 Processing helix chain 'Y' and resid 323 through 325 No H-bonds generated for 'chain 'Y' and resid 323 through 325' Processing helix chain 'Y' and resid 328 through 332 Processing helix chain 'Y' and resid 335 through 338 Processing helix chain 'Y' and resid 346 through 360 Processing helix chain 'Y' and resid 366 through 382 Processing helix chain 'Z' and resid 6 through 19 Processing helix chain 'Z' and resid 32 through 38 Processing helix chain 'Z' and resid 55 through 68 removed outlier: 3.736A pdb=" N GLU Z 60 " --> pdb=" O HIS Z 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 80 through 82 Processing sheet with id= B, first strand: chain '0' and resid 163 through 165 Processing sheet with id= C, first strand: chain '0' and resid 94 through 102 removed outlier: 6.696A pdb=" N TRP 0 115 " --> pdb=" O THR 0 98 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL 0 100 " --> pdb=" O LYS 0 113 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS 0 113 " --> pdb=" O VAL 0 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 150 through 153 Processing sheet with id= E, first strand: chain '6' and resid 179 through 184 removed outlier: 6.154A pdb=" N CYS 6 136 " --> pdb=" O VAL 6 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL 6 182 " --> pdb=" O CYS 6 136 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA 6 138 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP 6 184 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP 6 140 " --> pdb=" O ASP 6 184 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS 6 126 " --> pdb=" O TYR 6 139 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS 6 141 " --> pdb=" O LEU 6 124 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU 6 124 " --> pdb=" O LYS 6 141 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '7' and resid 349 through 353 removed outlier: 4.324A pdb=" N ALA 7 265 " --> pdb=" O PHE 7 192 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU 7 213 " --> pdb=" O LEU 7 189 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASP 7 191 " --> pdb=" O GLU 7 213 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N MET 7 215 " --> pdb=" O ASP 7 191 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '7' and resid 393 through 395 Processing sheet with id= H, first strand: chain '7' and resid 327 through 331 removed outlier: 6.774A pdb=" N ILE 7 373 " --> pdb=" O PHE 7 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '8' and resid 296 through 298 removed outlier: 4.784A pdb=" N GLY 8 151 " --> pdb=" O TYR 8 298 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA 8 148 " --> pdb=" O SER 8 63 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLN 8 344 " --> pdb=" O VAL 8 64 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU 8 66 " --> pdb=" O GLN 8 344 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE 8 346 " --> pdb=" O LEU 8 66 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '8' and resid 257 through 262 removed outlier: 6.882A pdb=" N LEU 8 197 " --> pdb=" O ARG 8 258 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR 8 260 " --> pdb=" O SER 8 195 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER 8 195 " --> pdb=" O THR 8 260 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N MET 8 262 " --> pdb=" O MET 8 193 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET 8 193 " --> pdb=" O MET 8 262 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N SER 8 239 " --> pdb=" O VAL 8 227 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL 8 227 " --> pdb=" O SER 8 239 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.637A pdb=" N LEU B 192 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE B 145 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B 194 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE B 195 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 220 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR B 234 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 223 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL B 236 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.859A pdb=" N ILE B 115 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER B 109 " --> pdb=" O HIS B 113 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N HIS B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 49 through 51 Processing sheet with id= N, first strand: chain 'C' and resid 109 through 111 Processing sheet with id= O, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.896A pdb=" N GLN C 156 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 254 through 261 removed outlier: 6.309A pdb=" N ALA D 246 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE D 222 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLY D 248 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR D 220 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 294 through 298 Processing sheet with id= R, first strand: chain 'D' and resid 370 through 372 removed outlier: 6.353A pdb=" N GLU D 372 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL D 383 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.051A pdb=" N LYS E 11 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL E 88 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 51 through 53 Processing sheet with id= U, first strand: chain 'E' and resid 35 through 41 removed outlier: 6.988A pdb=" N ASP E 67 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU E 39 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU E 65 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 156 through 162 removed outlier: 3.720A pdb=" N VAL F 170 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 197 through 199 Processing sheet with id= X, first strand: chain 'G' and resid 269 through 276 Processing sheet with id= Y, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.029A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR H 175 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU H 76 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR H 173 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL H 78 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU H 171 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL H 80 " --> pdb=" O ALA H 169 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA H 169 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 114 through 119 Processing sheet with id= AA, first strand: chain 'I' and resid 106 through 111 removed outlier: 6.652A pdb=" N VAL I 99 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE I 109 " --> pdb=" O ILE I 97 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE I 97 " --> pdb=" O PHE I 109 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER I 111 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR I 95 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU I 171 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL I 149 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE I 173 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 12.417A pdb=" N VAL I 151 " --> pdb=" O ILE I 173 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N ILE I 175 " --> pdb=" O VAL I 151 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 107 through 111 removed outlier: 6.826A pdb=" N ARG J 82 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR J 65 " --> pdb=" O CYS J 80 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N CYS J 80 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR J 67 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ARG J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 17 through 26 removed outlier: 6.462A pdb=" N ALA M 36 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN M 50 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 12 through 16 removed outlier: 8.558A pdb=" N LYS N 78 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE N 50 " --> pdb=" O LYS N 78 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU N 80 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS N 52 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG N 29 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL N 17 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 63 through 65 removed outlier: 6.422A pdb=" N LEU N 65 " --> pdb=" O ILE N 84 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE N 84 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 156 through 159 removed outlier: 6.463A pdb=" N LYS R 183 " --> pdb=" O VAL R 141 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL R 141 " --> pdb=" O LYS R 183 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 63 through 68 removed outlier: 6.726A pdb=" N TYR T 79 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET T 30 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG T 77 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL T 32 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE T 75 " --> pdb=" O VAL T 32 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'U' and resid 189 through 191 Processing sheet with id= AI, first strand: chain 'W' and resid 122 through 125 removed outlier: 3.617A pdb=" N HIS W 106 " --> pdb=" O TYR W 113 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP W 115 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE W 104 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS W 98 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY W 171 " --> pdb=" O ARG W 141 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG W 143 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU W 169 " --> pdb=" O ARG W 143 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'X' and resid 67 through 70 removed outlier: 4.443A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'X' and resid 341 through 345 removed outlier: 9.053A pdb=" N TYR X 124 " --> pdb=" O GLY X 304 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE X 306 " --> pdb=" O TYR X 124 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU X 126 " --> pdb=" O ILE X 306 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER X 308 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N GLY X 128 " --> pdb=" O SER X 308 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU X 258 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL X 307 " --> pdb=" O LEU X 258 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL X 260 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA X 309 " --> pdb=" O VAL X 260 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL X 262 " --> pdb=" O ALA X 309 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU X 151 " --> pdb=" O LEU X 259 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ALA X 261 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU X 153 " --> pdb=" O ALA X 261 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP X 263 " --> pdb=" O LEU X 153 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE X 155 " --> pdb=" O ASP X 263 " (cutoff:3.500A) 2032 hydrogen bonds defined for protein. 5715 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 579 hydrogen bonds 1050 hydrogen bond angles 0 basepair planarities 236 basepair parallelities 411 stacking parallelities Total time for adding SS restraints: 36.78 Time building geometry restraints manager: 25.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 28341 1.41 - 1.64: 41808 1.64 - 1.86: 394 1.86 - 2.09: 0 2.09 - 2.32: 20 Bond restraints: 70563 Sorted by residual: bond pdb=" N1 GDP X 503 " pdb=" C2 GDP X 503 " ideal model delta sigma weight residual 1.337 1.559 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C6 GDP X 503 " pdb=" O6 GDP X 503 " ideal model delta sigma weight residual 1.250 1.417 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" N7 MA6 A1584 " pdb=" C5 MA6 A1584 " ideal model delta sigma weight residual 1.356 1.517 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" N7 MA6 A1583 " pdb=" C5 MA6 A1583 " ideal model delta sigma weight residual 1.356 1.517 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C5A NAD A1738 " pdb=" N7A NAD A1738 " ideal model delta sigma weight residual 1.372 1.515 -0.143 2.00e-02 2.50e+03 5.14e+01 ... (remaining 70558 not shown) Histogram of bond angle deviations from ideal: 72.00 - 85.56: 16 85.56 - 99.12: 10 99.12 - 112.69: 43289 112.69 - 126.25: 52740 126.25 - 139.81: 3335 Bond angle restraints: 99390 Sorted by residual: angle pdb=" O1A NAD A1738 " pdb=" PA NAD A1738 " pdb=" O2A NAD A1738 " ideal model delta sigma weight residual 122.64 101.43 21.21 3.00e+00 1.11e-01 5.00e+01 angle pdb=" CA PRO 4 252 " pdb=" N PRO 4 252 " pdb=" CD PRO 4 252 " ideal model delta sigma weight residual 112.00 102.90 9.10 1.40e+00 5.10e-01 4.23e+01 angle pdb=" O1N NAD A1738 " pdb=" PN NAD A1738 " pdb=" O2N NAD A1738 " ideal model delta sigma weight residual 120.02 101.25 18.77 3.00e+00 1.11e-01 3.92e+01 angle pdb=" O3' MA6 A1583 " pdb=" P MA6 A1584 " pdb=" OP1 MA6 A1584 " ideal model delta sigma weight residual 108.00 90.90 17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" O3' G A1582 " pdb=" P MA6 A1583 " pdb=" OP1 MA6 A1583 " ideal model delta sigma weight residual 108.00 91.35 16.65 3.00e+00 1.11e-01 3.08e+01 ... (remaining 99385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 39874 35.75 - 71.49: 952 71.49 - 107.24: 103 107.24 - 142.98: 6 142.98 - 178.73: 9 Dihedral angle restraints: 40944 sinusoidal: 23206 harmonic: 17738 Sorted by residual: dihedral pdb=" CA LYS J 72 " pdb=" C LYS J 72 " pdb=" N PRO J 73 " pdb=" CA PRO J 73 " ideal model delta harmonic sigma weight residual 180.00 124.06 55.94 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" O4' U A1571 " pdb=" C1' U A1571 " pdb=" N1 U A1571 " pdb=" C2 U A1571 " ideal model delta sinusoidal sigma weight residual 200.00 26.01 173.99 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' C A 870 " pdb=" C1' C A 870 " pdb=" N1 C A 870 " pdb=" C2 C A 870 " ideal model delta sinusoidal sigma weight residual -160.00 8.94 -168.94 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 40941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.214: 11596 4.214 - 8.428: 0 8.428 - 12.642: 0 12.642 - 16.856: 0 16.856 - 21.070: 4 Chirality restraints: 11600 Sorted by residual: chirality pdb="FE3 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.51 -21.07 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S3 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.42 -20.98 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE4 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S3 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.38 20.94 2.00e-01 2.50e+01 1.10e+04 ... (remaining 11597 not shown) Planarity restraints: 9592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' MA6 A1584 " 0.032 2.00e-02 2.50e+03 5.72e-01 7.36e+03 pdb=" C4' MA6 A1584 " 0.437 2.00e-02 2.50e+03 pdb=" O4' MA6 A1584 " 0.647 2.00e-02 2.50e+03 pdb=" C3' MA6 A1584 " -0.594 2.00e-02 2.50e+03 pdb=" O3' MA6 A1584 " -0.563 2.00e-02 2.50e+03 pdb=" C2' MA6 A1584 " -0.212 2.00e-02 2.50e+03 pdb=" O2' MA6 A1584 " 0.897 2.00e-02 2.50e+03 pdb=" C1' MA6 A1584 " 0.228 2.00e-02 2.50e+03 pdb=" N9 MA6 A1584 " -0.872 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' MA6 A1583 " -0.026 2.00e-02 2.50e+03 5.32e-01 6.36e+03 pdb=" C4' MA6 A1583 " 0.423 2.00e-02 2.50e+03 pdb=" O4' MA6 A1583 " 0.673 2.00e-02 2.50e+03 pdb=" C3' MA6 A1583 " -0.586 2.00e-02 2.50e+03 pdb=" O3' MA6 A1583 " -0.440 2.00e-02 2.50e+03 pdb=" C2' MA6 A1583 " -0.268 2.00e-02 2.50e+03 pdb=" O2' MA6 A1583 " 0.784 2.00e-02 2.50e+03 pdb=" C1' MA6 A1583 " 0.235 2.00e-02 2.50e+03 pdb=" N9 MA6 A1583 " -0.795 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET 4 251 " 0.082 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO 4 252 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO 4 252 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO 4 252 " 0.063 5.00e-02 4.00e+02 ... (remaining 9589 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.59: 642 2.59 - 3.23: 62429 3.23 - 3.87: 145135 3.87 - 4.50: 197402 4.50 - 5.14: 285790 Nonbonded interactions: 691398 Sorted by model distance: nonbonded pdb=" OG SER X 171 " pdb=" OD1 ASP X 179 " model vdw 1.953 2.440 nonbonded pdb=" OP2 A A 882 " pdb="MG MG A1720 " model vdw 1.964 2.170 nonbonded pdb=" O2' C A 736 " pdb=" OP2 A A 738 " model vdw 1.980 2.440 nonbonded pdb=" OP1 C A 815 " pdb="MG MG A1719 " model vdw 1.990 2.170 nonbonded pdb="MG MG A1718 " pdb=" O HOH A1809 " model vdw 1.994 2.170 ... (remaining 691393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 17.510 Check model and map are aligned: 0.770 Set scattering table: 0.480 Process input model: 180.790 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.222 70563 Z= 0.237 Angle : 0.637 21.212 99390 Z= 0.324 Chirality : 0.391 21.070 11600 Planarity : 0.009 0.572 9592 Dihedral : 14.437 178.726 29438 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.39 % Favored : 98.59 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.44 (0.11), residues: 5969 helix: 1.82 (0.10), residues: 2871 sheet: -0.25 (0.20), residues: 617 loop : 0.38 (0.13), residues: 2481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1024 time to evaluate : 5.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 3 residues processed: 1025 average time/residue: 1.8163 time to fit residues: 2339.4419 Evaluate side-chains 694 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 691 time to evaluate : 5.128 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.6109 time to fit residues: 7.6812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 570 optimal weight: 7.9990 chunk 512 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 345 optimal weight: 0.4980 chunk 273 optimal weight: 10.0000 chunk 529 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 394 optimal weight: 8.9990 chunk 613 optimal weight: 1.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 32 GLN 0 111 HIS 0 192 ASN ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 489 HIS ** 4 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 157 GLN 6 165 HIS ** 6 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 GLN 7 60 HIS 7 69 ASN 7 98 HIS 7 398 HIS 7 400 HIS 8 222 ASN 8 249 GLN 8 270 HIS 8 302 HIS 8 308 HIS 8 313 HIS 8 353 GLN 8 376 GLN B 59 ASN B 157 ASN B 266 GLN C 154 HIS D 361 GLN E 41 ASN E 54 HIS E 57 GLN F 224 HIS G 127 HIS I 183 HIS L 77 GLN N 56 GLN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 221 GLN R 277 ASN R 278 ASN R 299 ASN R 308 HIS R 320 GLN T 37 HIS T 122 GLN U 43 ASN U 79 GLN U 161 GLN V 380 GLN V 399 GLN X 140 HIS X 159 HIS X 170 GLN Y 368 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.253 70563 Z= 0.361 Angle : 0.858 50.648 99390 Z= 0.506 Chirality : 0.124 6.416 11600 Planarity : 0.005 0.131 9592 Dihedral : 12.819 178.684 16848 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 5969 helix: 1.61 (0.10), residues: 2884 sheet: -0.13 (0.20), residues: 604 loop : 0.32 (0.13), residues: 2481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 702 time to evaluate : 5.310 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: 122 outliers final: 43 residues processed: 770 average time/residue: 1.7536 time to fit residues: 1711.3315 Evaluate side-chains 706 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 663 time to evaluate : 5.098 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 31 residues processed: 12 average time/residue: 1.0405 time to fit residues: 24.5407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 341 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 510 optimal weight: 8.9990 chunk 418 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 614 optimal weight: 4.9990 chunk 664 optimal weight: 8.9990 chunk 547 optimal weight: 0.3980 chunk 609 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 493 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 192 ASN ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 151 HIS 6 175 ASN 6 195 GLN ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 222 ASN D 361 GLN E 41 ASN F 216 GLN G 135 GLN H 83 HIS I 96 GLN L 77 GLN L 118 ASN O 65 GLN O 152 GLN O 221 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN X 201 GLN X 292 ASN Y 368 GLN ** Y 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.242 70563 Z= 0.246 Angle : 0.781 50.564 99390 Z= 0.474 Chirality : 0.123 6.379 11600 Planarity : 0.004 0.120 9592 Dihedral : 12.721 179.897 16848 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.49 (0.11), residues: 5969 helix: 1.83 (0.10), residues: 2883 sheet: -0.09 (0.20), residues: 607 loop : 0.39 (0.13), residues: 2479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 694 time to evaluate : 5.276 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: 116 outliers final: 45 residues processed: 759 average time/residue: 1.7478 time to fit residues: 1689.4272 Evaluate side-chains 696 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 651 time to evaluate : 5.183 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 34 residues processed: 11 average time/residue: 0.8482 time to fit residues: 21.0652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 607 optimal weight: 1.9990 chunk 462 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 412 optimal weight: 5.9990 chunk 617 optimal weight: 10.0000 chunk 653 optimal weight: 0.8980 chunk 322 optimal weight: 10.0000 chunk 584 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 GLN ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 204 HIS 8 222 ASN B 69 HIS D 361 GLN H 51 HIS L 77 GLN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 299 ASN R 320 GLN U 126 GLN V 377 GLN X 73 GLN ** X 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 201 GLN Y 368 GLN ** Y 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.239 70563 Z= 0.301 Angle : 0.808 50.574 99390 Z= 0.485 Chirality : 0.124 6.397 11600 Planarity : 0.005 0.120 9592 Dihedral : 12.702 177.617 16848 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.71 % Favored : 98.27 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.41 (0.11), residues: 5969 helix: 1.71 (0.10), residues: 2879 sheet: -0.01 (0.20), residues: 618 loop : 0.40 (0.13), residues: 2472 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 679 time to evaluate : 5.160 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: 135 outliers final: 56 residues processed: 765 average time/residue: 1.7945 time to fit residues: 1743.1739 Evaluate side-chains 700 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 644 time to evaluate : 5.162 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 41 residues processed: 15 average time/residue: 0.9385 time to fit residues: 27.7218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 544 optimal weight: 0.9980 chunk 370 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 486 optimal weight: 0.0470 chunk 269 optimal weight: 10.0000 chunk 557 optimal weight: 0.6980 chunk 451 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 333 optimal weight: 0.7980 chunk 586 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 346 HIS 4 545 GLN 6 195 GLN ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 222 ASN D 361 GLN F 216 GLN H 51 HIS O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN X 81 HIS X 201 GLN Y 378 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.241 70563 Z= 0.213 Angle : 0.760 50.547 99390 Z= 0.464 Chirality : 0.122 6.321 11600 Planarity : 0.004 0.114 9592 Dihedral : 12.607 176.440 16848 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.24 % Favored : 98.74 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.68 (0.11), residues: 5969 helix: 1.95 (0.10), residues: 2881 sheet: 0.09 (0.20), residues: 625 loop : 0.51 (0.13), residues: 2463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 698 time to evaluate : 5.195 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: 102 outliers final: 50 residues processed: 761 average time/residue: 1.7418 time to fit residues: 1699.2983 Evaluate side-chains 691 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 641 time to evaluate : 5.125 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 38 residues processed: 13 average time/residue: 0.9185 time to fit residues: 24.7362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 219 optimal weight: 10.0000 chunk 588 optimal weight: 3.9990 chunk 129 optimal weight: 0.0870 chunk 383 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 654 optimal weight: 3.9990 chunk 542 optimal weight: 7.9990 chunk 302 optimal weight: 8.9990 chunk 54 optimal weight: 0.0970 chunk 216 optimal weight: 8.9990 chunk 343 optimal weight: 5.9990 overall best weight: 2.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 192 ASN 6 170 GLN 6 195 GLN ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS I 141 GLN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 315 GLN R 320 GLN S 47 GLN V 358 GLN W 135 GLN X 201 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.238 70563 Z= 0.329 Angle : 0.820 50.557 99390 Z= 0.489 Chirality : 0.124 6.395 11600 Planarity : 0.005 0.120 9592 Dihedral : 12.573 175.607 16848 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.78 % Favored : 98.21 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.47 (0.11), residues: 5969 helix: 1.76 (0.10), residues: 2875 sheet: 0.07 (0.20), residues: 616 loop : 0.42 (0.13), residues: 2478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 653 time to evaluate : 5.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 63 residues processed: 730 average time/residue: 1.7741 time to fit residues: 1652.3774 Evaluate side-chains 708 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 645 time to evaluate : 5.143 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 45 residues processed: 18 average time/residue: 1.0158 time to fit residues: 33.3357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 630 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 372 optimal weight: 2.9990 chunk 477 optimal weight: 0.5980 chunk 370 optimal weight: 4.9990 chunk 550 optimal weight: 7.9990 chunk 365 optimal weight: 1.9990 chunk 651 optimal weight: 0.3980 chunk 407 optimal weight: 0.0570 chunk 397 optimal weight: 2.9990 chunk 300 optimal weight: 0.0470 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 157 GLN 6 195 GLN ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 HIS 7 107 GLN 8 241 HIS F 216 GLN H 109 HIS H 163 ASN I 141 GLN I 184 ASN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN V 358 GLN W 135 GLN X 73 GLN X 81 HIS X 201 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.240 70563 Z= 0.210 Angle : 0.761 50.541 99390 Z= 0.464 Chirality : 0.121 6.309 11600 Planarity : 0.004 0.113 9592 Dihedral : 12.503 174.956 16848 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.24 % Favored : 98.74 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.72 (0.11), residues: 5969 helix: 1.96 (0.10), residues: 2882 sheet: 0.18 (0.20), residues: 629 loop : 0.55 (0.13), residues: 2458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 686 time to evaluate : 5.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 47 residues processed: 752 average time/residue: 1.7688 time to fit residues: 1702.3169 Evaluate side-chains 687 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 640 time to evaluate : 5.179 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 41 residues processed: 7 average time/residue: 0.9567 time to fit residues: 16.6596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 403 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 389 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 414 optimal weight: 0.2980 chunk 443 optimal weight: 5.9990 chunk 322 optimal weight: 0.0040 chunk 60 optimal weight: 2.9990 chunk 512 optimal weight: 10.0000 overall best weight: 2.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 192 ASN 1 311 GLN ** 4 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 GLN ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 72 GLN 7 185 GLN I 141 GLN I 146 HIS I 184 ASN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN X 73 GLN X 201 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.238 70563 Z= 0.317 Angle : 0.809 50.525 99390 Z= 0.484 Chirality : 0.123 6.375 11600 Planarity : 0.005 0.119 9592 Dihedral : 12.441 174.381 16848 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.73 % Favored : 98.26 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.57 (0.11), residues: 5969 helix: 1.84 (0.10), residues: 2872 sheet: 0.14 (0.21), residues: 610 loop : 0.46 (0.13), residues: 2487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 643 time to evaluate : 5.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 49 residues processed: 706 average time/residue: 1.7745 time to fit residues: 1602.1726 Evaluate side-chains 675 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 626 time to evaluate : 5.239 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 45 residues processed: 4 average time/residue: 1.0779 time to fit residues: 12.9475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 592 optimal weight: 0.3980 chunk 624 optimal weight: 0.6980 chunk 569 optimal weight: 10.0000 chunk 607 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 476 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 548 optimal weight: 0.8980 chunk 574 optimal weight: 6.9990 chunk 605 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 192 ASN 1 311 GLN ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 GLN F 216 GLN I 141 GLN I 184 ASN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN X 201 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.240 70563 Z= 0.253 Angle : 0.784 50.558 99390 Z= 0.474 Chirality : 0.122 6.354 11600 Planarity : 0.004 0.117 9592 Dihedral : 12.425 173.727 16848 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.56 % Favored : 98.43 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.59 (0.11), residues: 5969 helix: 1.88 (0.10), residues: 2869 sheet: 0.12 (0.21), residues: 609 loop : 0.46 (0.13), residues: 2491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 644 time to evaluate : 5.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 53 residues processed: 699 average time/residue: 1.7604 time to fit residues: 1574.7929 Evaluate side-chains 681 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 628 time to evaluate : 5.226 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 43 residues processed: 10 average time/residue: 0.9334 time to fit residues: 20.7637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 398 optimal weight: 0.9990 chunk 642 optimal weight: 1.9990 chunk 391 optimal weight: 0.8980 chunk 304 optimal weight: 0.9980 chunk 446 optimal weight: 0.6980 chunk 673 optimal weight: 9.9990 chunk 619 optimal weight: 10.0000 chunk 536 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 192 ASN 1 311 GLN 4 540 HIS 6 195 GLN F 216 GLN H 161 GLN I 141 GLN I 184 ASN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN X 201 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.241 70563 Z= 0.231 Angle : 0.775 50.563 99390 Z= 0.470 Chirality : 0.122 6.336 11600 Planarity : 0.004 0.116 9592 Dihedral : 12.371 173.233 16848 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.57 % Favored : 98.41 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.67 (0.11), residues: 5969 helix: 1.94 (0.10), residues: 2874 sheet: 0.18 (0.21), residues: 608 loop : 0.49 (0.13), residues: 2487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11938 Ramachandran restraints generated. 5969 Oldfield, 0 Emsley, 5969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 639 time to evaluate : 5.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 50 residues processed: 687 average time/residue: 1.8027 time to fit residues: 1580.9091 Evaluate side-chains 670 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 620 time to evaluate : 5.183 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 43 residues processed: 8 average time/residue: 0.8451 time to fit residues: 17.1833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 425 optimal weight: 6.9990 chunk 571 optimal weight: 4.9990 chunk 164 optimal weight: 0.4980 chunk 494 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 149 optimal weight: 3.9990 chunk 537 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 551 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 311 GLN 6 195 GLN H 161 GLN I 141 GLN I 184 ASN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 312 GLN R 320 GLN X 201 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.147140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117211 restraints weight = 104631.169| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.40 r_work: 0.3411 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.004 0.241 70563 Z= 0.218 Angle : 0.764 50.557 99390 Z= 0.465 Chirality : 0.122 6.321 11600 Planarity : 0.004 0.115 9592 Dihedral : 12.303 173.722 16848 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.52 % Favored : 98.46 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 1.75 (0.11), residues: 5969 helix: 2.00 (0.10), residues: 2882 sheet: 0.24 (0.21), residues: 609 loop : 0.54 (0.13), residues: 2478 =============================================================================== Job complete usr+sys time: 26114.85 seconds wall clock time: 452 minutes 49.67 seconds (27169.67 seconds total)