Starting phenix.real_space_refine on Fri Feb 16 11:24:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/02_2024/8css_26969_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/02_2024/8css_26969.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/02_2024/8css_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_26969/02_2024/8css_26969_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/02_2024/8css_26969_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/02_2024/8css_26969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/02_2024/8css_26969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/02_2024/8css_26969_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8css_26969/02_2024/8css_26969_neut_updated.pdb" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.033 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 26.64, 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: 24.18 Conformation dependent library (CDL) restraints added in 7.0 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: 25.15 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: 38.58 Time building geometry restraints manager: 26.42 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: 41207 35.75 - 71.49: 2098 71.49 - 107.24: 323 107.24 - 142.98: 6 142.98 - 178.73: 9 Dihedral angle restraints: 43643 sinusoidal: 25905 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 43640 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: 3.900 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: 0.070 Extract box with map and model: 15.450 Check model and map are aligned: 0.730 Set scattering table: 0.480 Process input model: 191.670 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 226.290 ------------------------------------------------------------------------------- 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 : 18.561 178.726 32137 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 % Allowed : 0.11 % Favored : 99.87 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP 3 177 HIS 0.013 0.001 HIS 4 489 PHE 0.062 0.001 PHE 4 548 TYR 0.018 0.001 TYR D 281 ARG 0.012 0.001 ARG 4 160 *********************** 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 : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 269 MET cc_start: 0.8699 (mtp) cc_final: 0.8308 (mtm) REVERT: 6 106 ASP cc_start: 0.7186 (t70) cc_final: 0.6953 (t70) REVERT: B 64 ASN cc_start: 0.8535 (m110) cc_final: 0.8277 (m110) REVERT: B 102 MET cc_start: 0.9100 (mmm) cc_final: 0.8568 (mmm) REVERT: B 119 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7666 (mm-30) REVERT: C 20 GLU cc_start: 0.6394 (tt0) cc_final: 0.6147 (tp30) REVERT: D 361 GLN cc_start: 0.8820 (mt0) cc_final: 0.8536 (mt0) REVERT: D 424 ASN cc_start: 0.8324 (m-40) cc_final: 0.8114 (m-40) REVERT: E 76 GLU cc_start: 0.7789 (tt0) cc_final: 0.7577 (pm20) REVERT: G 168 MET cc_start: 0.8299 (mtp) cc_final: 0.8065 (mtp) REVERT: G 211 GLU cc_start: 0.7224 (mt-10) cc_final: 0.7005 (mt-10) REVERT: J 75 SER cc_start: 0.8610 (p) cc_final: 0.8364 (p) REVERT: K 103 ARG cc_start: 0.5697 (ttt180) cc_final: 0.5440 (tmt-80) REVERT: L 141 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7873 (mt-10) REVERT: L 169 ASN cc_start: 0.8740 (m-40) cc_final: 0.8525 (m-40) REVERT: M 85 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8171 (mtpt) REVERT: M 88 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8006 (mt-10) REVERT: N 23 GLN cc_start: 0.8453 (mt0) cc_final: 0.7814 (tt0) REVERT: Q 66 MET cc_start: 0.7524 (mtm) cc_final: 0.7287 (mtt) REVERT: R 86 ASN cc_start: 0.8127 (t0) cc_final: 0.7921 (t0) REVERT: S 98 ARG cc_start: 0.7440 (mtp85) cc_final: 0.7121 (mtp85) REVERT: S 133 ARG cc_start: 0.5522 (mtm-85) cc_final: 0.5259 (mtp-110) REVERT: T 3 MET cc_start: 0.8726 (mtp) cc_final: 0.8515 (mtp) REVERT: U 129 ARG cc_start: 0.6614 (mtm-85) cc_final: 0.6356 (mtt180) REVERT: W 110 ASN cc_start: 0.9024 (m-40) cc_final: 0.8753 (m-40) outliers start: 1 outliers final: 3 residues processed: 1025 average time/residue: 1.7946 time to fit residues: 2302.6037 Evaluate side-chains 694 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 691 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain X residue 266 ASN Chi-restraints excluded: chain Y residue 322 ASP 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 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 221 GLN O 225 GLN Q 79 ASN Q 85 GLN R 221 GLN R 277 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 ** both conformations clash, **PLEASE CHECK MANUALLY** V 380 GLN V 399 GLN X 140 HIS X 159 HIS Y 368 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.259 70563 Z= 0.360 Angle : 0.852 50.610 99390 Z= 0.504 Chirality : 0.123 6.325 11600 Planarity : 0.005 0.131 9592 Dihedral : 19.611 178.998 19553 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.23 % Allowed : 9.07 % Favored : 88.70 % 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: 1.31 (0.11), residues: 5969 helix: 1.65 (0.10), residues: 2883 sheet: -0.13 (0.20), residues: 604 loop : 0.34 (0.13), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP 3 177 HIS 0.014 0.002 HIS 4 489 PHE 0.032 0.002 PHE 4 548 TYR 0.025 0.002 TYR 4 559 ARG 0.007 0.001 ARG P 141 *********************** 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 822 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 703 time to evaluate : 5.647 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: 0 196 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8042 (mm) REVERT: 1 269 MET cc_start: 0.8676 (mtp) cc_final: 0.8375 (mtm) REVERT: 7 418 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7490 (ttp-170) REVERT: 8 104 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: B 102 MET cc_start: 0.9177 (mmm) cc_final: 0.8692 (mmm) REVERT: B 119 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7698 (mm-30) REVERT: C 20 GLU cc_start: 0.6482 (tt0) cc_final: 0.6179 (tp30) REVERT: D 361 GLN cc_start: 0.8870 (mt0) cc_final: 0.8568 (mt0) REVERT: D 424 ASN cc_start: 0.8395 (m-40) cc_final: 0.8131 (m-40) REVERT: F 239 TYR cc_start: 0.6759 (m-80) cc_final: 0.6349 (m-80) REVERT: G 122 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6621 (mpp80) REVERT: G 172 LEU cc_start: 0.7928 (mp) cc_final: 0.7705 (mt) REVERT: G 211 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7117 (mt-10) REVERT: G 243 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7676 (mtp180) REVERT: I 96 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: J 75 SER cc_start: 0.8944 (p) cc_final: 0.8713 (p) REVERT: K 102 ARG cc_start: 0.4856 (OUTLIER) cc_final: 0.4424 (mtm110) REVERT: L 166 MET cc_start: 0.8920 (mtm) cc_final: 0.8499 (mtp) REVERT: L 216 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: M 114 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7651 (mtt-85) REVERT: P 63 LYS cc_start: 0.7541 (tppt) cc_final: 0.7273 (tptp) REVERT: Q 66 MET cc_start: 0.7609 (mtm) cc_final: 0.7376 (mtt) REVERT: R 86 ASN cc_start: 0.8226 (t0) cc_final: 0.7975 (t0) REVERT: R 113 GLU cc_start: 0.6959 (tp30) cc_final: 0.6757 (tp30) REVERT: R 278 ASN cc_start: 0.8295 (m110) cc_final: 0.7917 (m110) REVERT: T 3 MET cc_start: 0.8983 (mtp) cc_final: 0.8595 (mtp) REVERT: T 110 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: U 134 ARG cc_start: 0.6747 (ttp-110) cc_final: 0.6416 (mtm110) REVERT: V 252 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8405 (mtmp) REVERT: W 109 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7255 (mt-10) REVERT: W 110 ASN cc_start: 0.9029 (m-40) cc_final: 0.8767 (m-40) outliers start: 119 outliers final: 46 residues processed: 769 average time/residue: 1.7557 time to fit residues: 1702.5288 Evaluate side-chains 725 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 669 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 4 residue 77 THR Chi-restraints excluded: chain 4 residue 258 SER Chi-restraints excluded: chain 4 residue 324 VAL Chi-restraints excluded: chain 4 residue 348 PHE Chi-restraints excluded: chain 4 residue 354 LEU Chi-restraints excluded: chain 4 residue 394 TYR Chi-restraints excluded: chain 4 residue 512 ILE Chi-restraints excluded: chain 6 residue 168 MET Chi-restraints excluded: chain 7 residue 36 GLN Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 194 SER Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 7 residue 418 ARG Chi-restraints excluded: chain 8 residue 104 GLU Chi-restraints excluded: chain 8 residue 202 SER Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 239 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain K residue 102 ARG Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain V residue 252 LYS Chi-restraints excluded: chain V residue 332 GLU Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 255 MET Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain Y residue 286 LEU Chi-restraints excluded: chain Y residue 288 THR Chi-restraints excluded: chain Y residue 349 HIS Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 34 VAL Chi-restraints excluded: chain Z residue 38 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 341 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 510 optimal weight: 0.8980 chunk 418 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 614 optimal weight: 4.9990 chunk 664 optimal weight: 7.9990 chunk 547 optimal weight: 6.9990 chunk 609 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 493 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 GLN 7 344 ASN 8 222 ASN B 59 ASN B 69 HIS E 41 ASN F 216 GLN G 135 GLN H 83 HIS L 77 GLN L 118 ASN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 299 ASN R 320 GLN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN X 292 ASN Y 368 GLN ** Y 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1678 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= 0.252 Angle : 0.786 50.506 99390 Z= 0.475 Chirality : 0.123 6.370 11600 Planarity : 0.004 0.120 9592 Dihedral : 19.529 179.041 19547 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.18 % Allowed : 10.61 % Favored : 87.22 % 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: 1.82 (0.10), residues: 2884 sheet: -0.08 (0.20), residues: 618 loop : 0.40 (0.13), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 1 234 HIS 0.008 0.001 HIS 7 52 PHE 0.026 0.001 PHE B 58 TYR 0.018 0.001 TYR V 91 ARG 0.008 0.000 ARG 0 195 *********************** 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 814 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 698 time to evaluate : 4.800 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: 0 196 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8015 (mm) REVERT: 1 269 MET cc_start: 0.8649 (mtp) cc_final: 0.8302 (mtm) REVERT: 4 595 MET cc_start: 0.6070 (mtp) cc_final: 0.5840 (mtm) REVERT: B 102 MET cc_start: 0.9165 (mmm) cc_final: 0.8712 (mmm) REVERT: B 119 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7687 (mm-30) REVERT: C 20 GLU cc_start: 0.6536 (tt0) cc_final: 0.6224 (tp30) REVERT: D 190 GLU cc_start: 0.5069 (OUTLIER) cc_final: 0.4675 (pp20) REVERT: D 361 GLN cc_start: 0.8906 (mt0) cc_final: 0.8587 (mt0) REVERT: D 424 ASN cc_start: 0.8289 (m-40) cc_final: 0.8060 (m-40) REVERT: F 239 TYR cc_start: 0.6810 (m-80) cc_final: 0.6403 (m-80) REVERT: G 122 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7288 (mtp85) REVERT: G 172 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7670 (mt) REVERT: G 211 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7036 (mt-10) REVERT: G 243 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7684 (mtp180) REVERT: J 75 SER cc_start: 0.8887 (p) cc_final: 0.8638 (p) REVERT: L 166 MET cc_start: 0.8915 (mtm) cc_final: 0.8501 (mtp) REVERT: L 216 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: N 23 GLN cc_start: 0.8408 (mt0) cc_final: 0.7766 (tt0) REVERT: P 63 LYS cc_start: 0.7523 (tppt) cc_final: 0.7260 (tptp) REVERT: P 141 ARG cc_start: 0.6206 (mtm-85) cc_final: 0.5962 (mtp180) REVERT: Q 66 MET cc_start: 0.7600 (mtm) cc_final: 0.7362 (mtt) REVERT: R 86 ASN cc_start: 0.8214 (t0) cc_final: 0.7975 (t0) REVERT: R 113 GLU cc_start: 0.6992 (tp30) cc_final: 0.6727 (tp30) REVERT: R 278 ASN cc_start: 0.8296 (m110) cc_final: 0.7969 (m110) REVERT: S 50 ARG cc_start: 0.7787 (mtt-85) cc_final: 0.7533 (mtt-85) REVERT: T 3 MET cc_start: 0.8990 (mtp) cc_final: 0.8612 (mtp) REVERT: T 110 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: U 57 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7645 (mtp) REVERT: U 93 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6812 (ttp-110) REVERT: U 185 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8362 (tmtm) REVERT: V 38 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.7013 (m90) REVERT: W 110 ASN cc_start: 0.9014 (m-40) cc_final: 0.8708 (m-40) REVERT: W 143 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7823 (ttm-80) outliers start: 116 outliers final: 37 residues processed: 758 average time/residue: 1.7331 time to fit residues: 1655.9058 Evaluate side-chains 703 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 655 time to evaluate : 4.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 3 residue 158 GLN Chi-restraints excluded: chain 4 residue 77 THR Chi-restraints excluded: chain 4 residue 283 LEU Chi-restraints excluded: chain 4 residue 292 TYR Chi-restraints excluded: chain 4 residue 348 PHE Chi-restraints excluded: chain 4 residue 354 LEU Chi-restraints excluded: chain 4 residue 512 ILE Chi-restraints excluded: chain 4 residue 641 ILE Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 194 SER Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 8 residue 202 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 180 LYS Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain U residue 57 MET Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 38 HIS Chi-restraints excluded: chain V residue 332 GLU Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 255 MET Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain Y residue 349 HIS Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 34 VAL 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: 4.9990 chunk 319 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 412 optimal weight: 5.9990 chunk 617 optimal weight: 8.9990 chunk 653 optimal weight: 0.7980 chunk 322 optimal weight: 10.0000 chunk 584 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 346 HIS ** 4 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 175 ASN 6 195 GLN 7 204 HIS 8 222 ASN H 51 HIS I 96 GLN L 77 GLN O 65 GLN O 152 GLN O 225 GLN Q 79 ASN Q 85 GLN R 299 ASN R 320 GLN S 47 GLN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 377 GLN X 73 GLN ** X 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 201 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 368 GLN Y 378 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2019 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 : 0.822 50.563 99390 Z= 0.491 Chirality : 0.124 6.405 11600 Planarity : 0.005 0.121 9592 Dihedral : 19.538 176.101 19547 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.83 % Favored : 98.16 % Rotamer: Outliers : 2.67 % Allowed : 11.41 % Favored : 85.92 % 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: 1.36 (0.11), residues: 5969 helix: 1.67 (0.10), residues: 2878 sheet: -0.02 (0.20), residues: 616 loop : 0.37 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 1 234 HIS 0.009 0.001 HIS X 81 PHE 0.027 0.002 PHE 7 43 TYR 0.022 0.002 TYR V 91 ARG 0.007 0.001 ARG C 152 *********************** 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 823 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 681 time to evaluate : 4.869 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: 0 196 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8111 (mm) REVERT: 1 269 MET cc_start: 0.8619 (mtp) cc_final: 0.8399 (mtm) REVERT: 3 172 ASP cc_start: 0.8329 (t70) cc_final: 0.8043 (t0) REVERT: 4 299 GLU cc_start: 0.6214 (mt-10) cc_final: 0.5941 (tp30) REVERT: 4 530 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: 4 582 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6254 (mm) REVERT: 6 92 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6386 (ttp-110) REVERT: 8 108 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.6723 (m90) REVERT: B 102 MET cc_start: 0.9185 (mmm) cc_final: 0.8599 (mmt) REVERT: B 119 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 232 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8815 (mt) REVERT: C 20 GLU cc_start: 0.6604 (tt0) cc_final: 0.6262 (tp30) REVERT: D 190 GLU cc_start: 0.5028 (OUTLIER) cc_final: 0.4645 (pp20) REVERT: D 361 GLN cc_start: 0.8866 (mt0) cc_final: 0.8546 (mt0) REVERT: D 424 ASN cc_start: 0.8304 (m-40) cc_final: 0.8049 (m-40) REVERT: F 239 TYR cc_start: 0.6833 (m-80) cc_final: 0.6359 (m-80) REVERT: G 122 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7318 (mtp85) REVERT: G 172 LEU cc_start: 0.7921 (mp) cc_final: 0.7669 (mt) REVERT: G 211 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7153 (mt-10) REVERT: J 75 SER cc_start: 0.8966 (p) cc_final: 0.8714 (p) REVERT: L 107 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8329 (mttm) REVERT: L 109 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: L 166 MET cc_start: 0.8943 (mtm) cc_final: 0.8578 (mtp) REVERT: L 216 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: L 217 THR cc_start: 0.8651 (m) cc_final: 0.8448 (m) REVERT: M 114 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7664 (mtt-85) REVERT: N 23 GLN cc_start: 0.8381 (mt0) cc_final: 0.7741 (tt0) REVERT: P 63 LYS cc_start: 0.7495 (tppt) cc_final: 0.7238 (tptp) REVERT: Q 66 MET cc_start: 0.7640 (mtm) cc_final: 0.7385 (mtt) REVERT: R 86 ASN cc_start: 0.8294 (t0) cc_final: 0.8044 (t0) REVERT: R 113 GLU cc_start: 0.6948 (tp30) cc_final: 0.6711 (tp30) REVERT: S 27 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: S 55 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7274 (ptpt) REVERT: S 98 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7428 (mtp180) REVERT: T 3 MET cc_start: 0.9013 (mtp) cc_final: 0.8580 (mtp) REVERT: T 110 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: U 93 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6853 (ttp-110) REVERT: U 185 LYS cc_start: 0.8553 (tmtt) cc_final: 0.8315 (tmtm) REVERT: V 29 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7806 (mp) REVERT: V 340 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7999 (ttmt) REVERT: W 110 ASN cc_start: 0.8955 (m-40) cc_final: 0.8672 (m-40) REVERT: W 143 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: X 176 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7125 (mt0) outliers start: 142 outliers final: 57 residues processed: 770 average time/residue: 1.7698 time to fit residues: 1717.8650 Evaluate side-chains 723 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 646 time to evaluate : 4.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 121 LYS Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 1 residue 239 TRP Chi-restraints excluded: chain 3 residue 158 GLN Chi-restraints excluded: chain 4 residue 77 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 283 LEU Chi-restraints excluded: chain 4 residue 292 TYR Chi-restraints excluded: chain 4 residue 348 PHE Chi-restraints excluded: chain 4 residue 354 LEU Chi-restraints excluded: chain 4 residue 394 TYR Chi-restraints excluded: chain 4 residue 512 ILE Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 582 LEU Chi-restraints excluded: chain 4 residue 589 THR Chi-restraints excluded: chain 4 residue 641 ILE Chi-restraints excluded: chain 6 residue 92 ARG Chi-restraints excluded: chain 6 residue 126 LYS Chi-restraints excluded: chain 6 residue 201 ASP Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 7 residue 194 SER Chi-restraints excluded: chain 8 residue 108 HIS Chi-restraints excluded: chain 8 residue 189 VAL Chi-restraints excluded: chain 8 residue 202 SER Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 180 LYS Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 332 GLU Chi-restraints excluded: chain V residue 340 LYS Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 176 GLN Chi-restraints excluded: chain X residue 255 MET Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain Y residue 349 HIS Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 33 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 544 optimal weight: 4.9990 chunk 370 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 486 optimal weight: 0.7980 chunk 269 optimal weight: 10.0000 chunk 557 optimal weight: 6.9990 chunk 451 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 chunk 586 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 192 ASN 0 194 GLN 4 545 GLN 6 195 GLN 8 222 ASN F 216 GLN H 51 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 U 126 GLN V 358 GLN X 81 HIS X 201 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2011 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= 0.224 Angle : 0.769 50.568 99390 Z= 0.468 Chirality : 0.122 6.340 11600 Planarity : 0.004 0.115 9592 Dihedral : 19.429 174.554 19547 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.31 % Favored : 98.68 % Rotamer: Outliers : 1.84 % Allowed : 12.97 % Favored : 85.19 % 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: 1.86 (0.10), residues: 2889 sheet: 0.03 (0.20), residues: 617 loop : 0.45 (0.13), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 4 313 HIS 0.009 0.001 HIS 7 52 PHE 0.020 0.001 PHE 4 548 TYR 0.016 0.001 TYR V 91 ARG 0.021 0.000 ARG Z 10 *********************** 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 775 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 677 time to evaluate : 4.898 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: 0 196 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8082 (mm) REVERT: 1 269 MET cc_start: 0.8602 (mtp) cc_final: 0.8233 (mtm) REVERT: 3 172 ASP cc_start: 0.8280 (t70) cc_final: 0.8066 (t0) REVERT: 4 299 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5876 (tp30) REVERT: 4 394 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: 4 530 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: 4 582 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.6094 (mm) REVERT: B 102 MET cc_start: 0.9156 (mmm) cc_final: 0.8724 (mmm) REVERT: B 119 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7687 (mm-30) REVERT: D 190 GLU cc_start: 0.5041 (OUTLIER) cc_final: 0.4650 (pp20) REVERT: D 361 GLN cc_start: 0.8900 (mt0) cc_final: 0.8575 (mt0) REVERT: F 239 TYR cc_start: 0.6825 (m-80) cc_final: 0.6397 (m-80) REVERT: G 122 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7238 (mtp85) REVERT: G 172 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7675 (mt) REVERT: G 211 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7105 (mt-10) REVERT: H 113 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7543 (ptt-90) REVERT: J 75 SER cc_start: 0.8841 (p) cc_final: 0.8581 (p) REVERT: L 166 MET cc_start: 0.8909 (mtm) cc_final: 0.8457 (mtp) REVERT: L 216 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: M 13 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6828 (ttt-90) REVERT: N 23 GLN cc_start: 0.8385 (mt0) cc_final: 0.7753 (tt0) REVERT: P 63 LYS cc_start: 0.7511 (tppt) cc_final: 0.7265 (tptp) REVERT: Q 66 MET cc_start: 0.7613 (mtm) cc_final: 0.7378 (mtt) REVERT: R 86 ASN cc_start: 0.8233 (t0) cc_final: 0.7999 (t0) REVERT: R 113 GLU cc_start: 0.6925 (tp30) cc_final: 0.6716 (tp30) REVERT: S 98 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7457 (mtp180) REVERT: T 3 MET cc_start: 0.9004 (mtp) cc_final: 0.8563 (mtp) REVERT: T 110 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: U 93 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6805 (ttp-110) REVERT: V 340 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.8001 (ttmt) REVERT: W 110 ASN cc_start: 0.9043 (m-40) cc_final: 0.8748 (m-40) REVERT: W 143 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7722 (ttm-80) outliers start: 98 outliers final: 32 residues processed: 732 average time/residue: 1.7559 time to fit residues: 1624.2581 Evaluate side-chains 692 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 646 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 3 residue 131 LEU Chi-restraints excluded: chain 3 residue 158 GLN Chi-restraints excluded: chain 4 residue 77 THR Chi-restraints excluded: chain 4 residue 292 TYR Chi-restraints excluded: chain 4 residue 348 PHE Chi-restraints excluded: chain 4 residue 394 TYR Chi-restraints excluded: chain 4 residue 512 ILE Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 582 LEU Chi-restraints excluded: chain 6 residue 153 GLU Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 8 residue 189 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain V residue 332 GLU Chi-restraints excluded: chain V residue 340 LYS Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain Y residue 349 HIS Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 34 VAL 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: 2.9990 chunk 129 optimal weight: 6.9990 chunk 383 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 654 optimal weight: 0.9990 chunk 542 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 6 195 GLN 7 72 GLN B 69 HIS H 51 HIS H 163 ASN I 141 GLN I 184 ASN L 146 HIS 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 W 135 GLN X 201 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.236 70563 Z= 0.386 Angle : 0.853 50.584 99390 Z= 0.503 Chirality : 0.125 6.423 11600 Planarity : 0.005 0.122 9592 Dihedral : 19.476 175.504 19547 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 2.68 % Allowed : 12.84 % Favored : 84.48 % 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: 1.25 (0.11), residues: 5969 helix: 1.57 (0.10), residues: 2874 sheet: -0.04 (0.20), residues: 619 loop : 0.32 (0.13), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP 1 239 HIS 0.007 0.001 HIS 7 175 PHE 0.030 0.002 PHE 7 43 TYR 0.024 0.002 TYR V 91 ARG 0.012 0.001 ARG H 75 *********************** 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 801 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 658 time to evaluate : 4.807 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: 0 196 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8170 (mm) REVERT: 1 269 MET cc_start: 0.8594 (mtp) cc_final: 0.8271 (mtm) REVERT: 3 131 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8347 (mm) REVERT: 3 172 ASP cc_start: 0.8356 (t70) cc_final: 0.8068 (t0) REVERT: 4 530 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: 4 582 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6240 (mm) REVERT: 6 92 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7153 (ttp-110) REVERT: 8 272 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6973 (ptm-80) REVERT: B 102 MET cc_start: 0.9177 (mmm) cc_final: 0.8592 (mmt) REVERT: B 119 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 232 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8789 (mt) REVERT: D 190 GLU cc_start: 0.4995 (OUTLIER) cc_final: 0.4557 (pp20) REVERT: D 361 GLN cc_start: 0.8856 (mt0) cc_final: 0.8542 (mt0) REVERT: F 239 TYR cc_start: 0.6936 (m-80) cc_final: 0.6464 (m-80) REVERT: G 122 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7351 (mtp85) REVERT: G 172 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7696 (mt) REVERT: G 211 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7123 (mt-10) REVERT: H 113 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7573 (ptm-80) REVERT: H 117 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6079 (mtt180) REVERT: J 75 SER cc_start: 0.9002 (p) cc_final: 0.8742 (p) REVERT: L 166 MET cc_start: 0.8948 (mtm) cc_final: 0.8612 (mtp) REVERT: L 216 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: L 217 THR cc_start: 0.8655 (m) cc_final: 0.8447 (m) REVERT: L 225 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5772 (ttp-170) REVERT: M 114 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7717 (mtt-85) REVERT: N 23 GLN cc_start: 0.8370 (mt0) cc_final: 0.7725 (tt0) REVERT: P 63 LYS cc_start: 0.7511 (tppt) cc_final: 0.7249 (tptp) REVERT: Q 66 MET cc_start: 0.7645 (mtm) cc_final: 0.7411 (mtt) REVERT: R 113 GLU cc_start: 0.6948 (tp30) cc_final: 0.6717 (tp30) REVERT: R 213 GLU cc_start: 0.7289 (mp0) cc_final: 0.6726 (pm20) REVERT: S 27 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: S 55 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7327 (ptpt) REVERT: T 3 MET cc_start: 0.9038 (mtp) cc_final: 0.8564 (mtp) REVERT: T 110 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: U 93 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6866 (ttp-110) REVERT: V 29 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7885 (mp) REVERT: V 155 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6776 (mm-30) REVERT: V 340 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7987 (ttmt) REVERT: V 401 LYS cc_start: 0.6355 (OUTLIER) cc_final: 0.5968 (pttt) REVERT: W 110 ASN cc_start: 0.8960 (m-40) cc_final: 0.8690 (m-40) REVERT: W 143 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8190 (ttm110) REVERT: X 100 MET cc_start: 0.9027 (ttm) cc_final: 0.8775 (ttp) REVERT: X 176 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7110 (mt0) outliers start: 143 outliers final: 69 residues processed: 742 average time/residue: 1.7636 time to fit residues: 1652.4916 Evaluate side-chains 733 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 639 time to evaluate : 4.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 39 GLU Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 3 residue 131 LEU Chi-restraints excluded: chain 3 residue 158 GLN Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 283 LEU Chi-restraints excluded: chain 4 residue 292 TYR Chi-restraints excluded: chain 4 residue 348 PHE Chi-restraints excluded: chain 4 residue 394 TYR Chi-restraints excluded: chain 4 residue 512 ILE Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 582 LEU Chi-restraints excluded: chain 6 residue 92 ARG Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 8 residue 189 VAL Chi-restraints excluded: chain 8 residue 202 SER Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 263 LEU Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 58 ARG Chi-restraints excluded: chain K residue 112 ARG Chi-restraints excluded: chain L residue 88 VAL Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 180 LYS Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain L residue 225 ARG Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 56 GLN Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain U residue 57 MET Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 155 GLU Chi-restraints excluded: chain V residue 332 GLU Chi-restraints excluded: chain V residue 340 LYS Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain V residue 401 LYS Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 172 ILE Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 176 GLN Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain Y residue 347 ILE Chi-restraints excluded: chain Y residue 349 HIS Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 34 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 630 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 372 optimal weight: 7.9990 chunk 477 optimal weight: 6.9990 chunk 370 optimal weight: 3.9990 chunk 550 optimal weight: 8.9990 chunk 365 optimal weight: 0.9980 chunk 651 optimal weight: 1.9990 chunk 407 optimal weight: 0.0570 chunk 397 optimal weight: 0.7980 chunk 300 optimal weight: 3.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 6 195 GLN 7 49 HIS 8 222 ASN F 216 GLN H 51 HIS H 109 HIS I 141 GLN I 184 ASN L 118 ASN O 65 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 81 HIS ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 378 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2247 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= 0.225 Angle : 0.775 50.568 99390 Z= 0.470 Chirality : 0.122 6.332 11600 Planarity : 0.004 0.114 9592 Dihedral : 19.367 173.546 19547 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.44 % Favored : 98.54 % Rotamer: Outliers : 1.86 % Allowed : 13.82 % Favored : 84.33 % 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: 1.56 (0.11), residues: 5969 helix: 1.88 (0.10), residues: 2860 sheet: -0.02 (0.21), residues: 616 loop : 0.44 (0.13), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 4 313 HIS 0.009 0.001 HIS 7 52 PHE 0.020 0.001 PHE Y 380 TYR 0.018 0.001 TYR V 91 ARG 0.010 0.000 ARG Q 28 *********************** 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 774 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 675 time to evaluate : 4.992 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: 0 196 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8114 (mm) REVERT: 1 269 MET cc_start: 0.8592 (mtp) cc_final: 0.8203 (mtm) REVERT: 3 172 ASP cc_start: 0.8292 (t70) cc_final: 0.8072 (t0) REVERT: 4 530 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: B 102 MET cc_start: 0.9147 (mmm) cc_final: 0.8698 (mmm) REVERT: B 119 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7697 (mm-30) REVERT: D 361 GLN cc_start: 0.8896 (mt0) cc_final: 0.8571 (mt0) REVERT: F 239 TYR cc_start: 0.6862 (m-80) cc_final: 0.6479 (m-80) REVERT: G 122 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7213 (mtp85) REVERT: G 172 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7684 (mt) REVERT: G 211 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7122 (mt-10) REVERT: G 220 GLN cc_start: 0.7784 (mt0) cc_final: 0.7564 (tt0) REVERT: J 75 SER cc_start: 0.8865 (p) cc_final: 0.8589 (p) REVERT: L 166 MET cc_start: 0.8912 (mtm) cc_final: 0.8502 (mtp) REVERT: L 216 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: M 13 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6807 (ttt-90) REVERT: M 114 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7723 (mtt-85) REVERT: N 23 GLN cc_start: 0.8349 (mt0) cc_final: 0.7730 (tt0) REVERT: P 63 LYS cc_start: 0.7494 (tppt) cc_final: 0.7248 (tptp) REVERT: Q 66 MET cc_start: 0.7637 (mtm) cc_final: 0.7390 (mtt) REVERT: R 81 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7519 (ttpp) REVERT: R 113 GLU cc_start: 0.6911 (tp30) cc_final: 0.6680 (tp30) REVERT: R 213 GLU cc_start: 0.7270 (mp0) cc_final: 0.6702 (pm20) REVERT: T 3 MET cc_start: 0.9024 (mtp) cc_final: 0.8552 (mtp) REVERT: T 110 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: U 93 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6829 (ttp-110) REVERT: V 29 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7788 (mp) REVERT: V 155 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6726 (mm-30) REVERT: V 401 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.5905 (pttt) REVERT: W 110 ASN cc_start: 0.8967 (m-40) cc_final: 0.8665 (m-40) REVERT: W 143 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7751 (ttm-80) outliers start: 99 outliers final: 46 residues processed: 732 average time/residue: 1.8476 time to fit residues: 1731.4149 Evaluate side-chains 702 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 642 time to evaluate : 4.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 3 residue 158 GLN Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 283 LEU Chi-restraints excluded: chain 4 residue 291 VAL Chi-restraints excluded: chain 4 residue 292 TYR Chi-restraints excluded: chain 4 residue 348 PHE Chi-restraints excluded: chain 4 residue 394 TYR Chi-restraints excluded: chain 4 residue 512 ILE Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 6 residue 153 GLU Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 189 VAL Chi-restraints excluded: chain 8 residue 363 MET Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 155 GLU Chi-restraints excluded: chain V residue 332 GLU Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain V residue 401 LYS Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 172 ILE Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain Y residue 349 HIS Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 34 VAL 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: 6.9990 chunk 196 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 414 optimal weight: 5.9990 chunk 443 optimal weight: 5.9990 chunk 322 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 512 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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** 6 157 GLN 6 195 GLN 7 107 GLN 7 185 GLN ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN I 141 GLN I 184 ASN O 65 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 380 GLN W 135 GLN X 201 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 372 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.236 70563 Z= 0.415 Angle : 0.868 50.561 99390 Z= 0.509 Chirality : 0.125 6.428 11600 Planarity : 0.005 0.123 9592 Dihedral : 19.459 176.225 19547 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.03 % Favored : 97.96 % Rotamer: Outliers : 2.22 % Allowed : 14.04 % Favored : 83.74 % 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: 1.18 (0.11), residues: 5969 helix: 1.52 (0.10), residues: 2867 sheet: -0.06 (0.20), residues: 616 loop : 0.28 (0.13), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 4 313 HIS 0.007 0.001 HIS 7 175 PHE 0.026 0.002 PHE 7 43 TYR 0.035 0.002 TYR 4 259 ARG 0.014 0.001 ARG H 75 *********************** 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 762 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 644 time to evaluate : 4.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 196 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8182 (mm) REVERT: 1 269 MET cc_start: 0.8580 (mtp) cc_final: 0.8262 (mtm) REVERT: 3 172 ASP cc_start: 0.8387 (t70) cc_final: 0.8094 (t0) REVERT: 4 391 PHE cc_start: 0.5066 (OUTLIER) cc_final: 0.4596 (p90) REVERT: 4 530 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: 4 582 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6212 (mm) REVERT: 6 92 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7322 (ttp-110) REVERT: B 102 MET cc_start: 0.9168 (mmm) cc_final: 0.8580 (mmt) REVERT: B 119 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7720 (mm-30) REVERT: B 232 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8793 (mt) REVERT: D 361 GLN cc_start: 0.8858 (mt0) cc_final: 0.8544 (mt0) REVERT: G 122 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7387 (mtp85) REVERT: G 172 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7731 (mt) REVERT: G 211 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7180 (mt-10) REVERT: G 220 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: H 113 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7575 (ptm-80) REVERT: J 75 SER cc_start: 0.9008 (p) cc_final: 0.8737 (p) REVERT: K 102 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.4874 (mtm110) REVERT: L 166 MET cc_start: 0.8949 (mtm) cc_final: 0.8535 (mtp) REVERT: L 216 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: L 217 THR cc_start: 0.8663 (m) cc_final: 0.8454 (m) REVERT: M 114 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7706 (mtt-85) REVERT: N 23 GLN cc_start: 0.8368 (mt0) cc_final: 0.7723 (tt0) REVERT: P 63 LYS cc_start: 0.7504 (tppt) cc_final: 0.7214 (tptp) REVERT: Q 66 MET cc_start: 0.7631 (mtm) cc_final: 0.7392 (mtt) REVERT: R 81 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7486 (ttpp) REVERT: R 113 GLU cc_start: 0.6982 (tp30) cc_final: 0.6739 (tp30) REVERT: R 213 GLU cc_start: 0.7308 (mp0) cc_final: 0.6735 (pm20) REVERT: S 28 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8623 (mtmt) REVERT: S 55 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7283 (ptpt) REVERT: T 3 MET cc_start: 0.9045 (mtp) cc_final: 0.8574 (mtp) REVERT: T 110 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: U 93 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6875 (ttp-110) REVERT: V 29 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7887 (mp) REVERT: V 155 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6753 (mm-30) REVERT: V 340 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7988 (ttmt) REVERT: V 401 LYS cc_start: 0.6439 (pptt) cc_final: 0.5981 (pttt) REVERT: W 110 ASN cc_start: 0.8972 (m-40) cc_final: 0.8689 (m-40) REVERT: W 143 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8200 (ttm110) REVERT: X 100 MET cc_start: 0.9030 (ttm) cc_final: 0.8795 (ttp) REVERT: X 176 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7146 (mt0) outliers start: 118 outliers final: 62 residues processed: 717 average time/residue: 1.7669 time to fit residues: 1595.6638 Evaluate side-chains 716 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 631 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 39 GLU Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 1 residue 138 ASP Chi-restraints excluded: chain 3 residue 158 GLN Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 145 PHE Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 283 LEU Chi-restraints excluded: chain 4 residue 291 VAL Chi-restraints excluded: chain 4 residue 292 TYR Chi-restraints excluded: chain 4 residue 320 LEU Chi-restraints excluded: chain 4 residue 348 PHE Chi-restraints excluded: chain 4 residue 391 PHE Chi-restraints excluded: chain 4 residue 394 TYR Chi-restraints excluded: chain 4 residue 512 ILE Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 582 LEU Chi-restraints excluded: chain 4 residue 589 THR Chi-restraints excluded: chain 6 residue 92 ARG Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 6 residue 153 GLU Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 7 residue 107 GLN Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 8 residue 189 VAL Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 102 ARG Chi-restraints excluded: chain K residue 112 ARG Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 180 LYS Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 206 LYS Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 155 GLU Chi-restraints excluded: chain V residue 332 GLU Chi-restraints excluded: chain V residue 340 LYS Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 172 ILE Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 176 GLN Chi-restraints excluded: chain X residue 255 MET Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain Y residue 349 HIS Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 592 optimal weight: 0.7980 chunk 624 optimal weight: 2.9990 chunk 569 optimal weight: 3.9990 chunk 607 optimal weight: 2.9990 chunk 365 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 476 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 548 optimal weight: 4.9990 chunk 574 optimal weight: 7.9990 chunk 605 optimal weight: 0.3980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 6 195 GLN 8 222 ASN 8 241 HIS F 216 GLN I 141 GLN I 184 ASN L 118 ASN O 65 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 378 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 70563 Z= 0.279 Angle : 0.808 50.561 99390 Z= 0.484 Chirality : 0.123 6.368 11600 Planarity : 0.005 0.117 9592 Dihedral : 19.424 173.173 19547 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.69 % Favored : 98.29 % Rotamer: Outliers : 1.67 % Allowed : 14.89 % Favored : 83.44 % 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: 1.32 (0.11), residues: 5969 helix: 1.67 (0.10), residues: 2857 sheet: -0.10 (0.20), residues: 626 loop : 0.34 (0.13), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 4 313 HIS 0.008 0.001 HIS 7 52 PHE 0.018 0.001 PHE 4 548 TYR 0.020 0.001 TYR V 91 ARG 0.017 0.000 ARG Q 28 *********************** 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 739 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 650 time to evaluate : 5.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 196 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8185 (mm) REVERT: 1 269 MET cc_start: 0.8565 (mtp) cc_final: 0.8212 (mtm) REVERT: 3 172 ASP cc_start: 0.8367 (t70) cc_final: 0.8063 (t0) REVERT: 4 391 PHE cc_start: 0.5211 (OUTLIER) cc_final: 0.4662 (p90) REVERT: 4 530 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: B 58 PHE cc_start: 0.7185 (t80) cc_final: 0.6754 (t80) REVERT: B 102 MET cc_start: 0.9165 (mmm) cc_final: 0.8704 (mmm) REVERT: B 119 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7707 (mm-30) REVERT: D 361 GLN cc_start: 0.8860 (mt0) cc_final: 0.8537 (mt0) REVERT: F 239 TYR cc_start: 0.6949 (m-80) cc_final: 0.6570 (m-80) REVERT: G 122 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7385 (mtp85) REVERT: G 172 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7691 (mt) REVERT: G 211 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7153 (mt-10) REVERT: G 220 GLN cc_start: 0.7858 (mt0) cc_final: 0.7637 (tt0) REVERT: H 113 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7564 (ptm-80) REVERT: J 75 SER cc_start: 0.8932 (p) cc_final: 0.8646 (p) REVERT: K 102 ARG cc_start: 0.5172 (OUTLIER) cc_final: 0.4797 (mtm110) REVERT: L 166 MET cc_start: 0.8939 (mtm) cc_final: 0.8535 (mtp) REVERT: L 216 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: L 217 THR cc_start: 0.8633 (m) cc_final: 0.8425 (m) REVERT: M 114 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7745 (mtt-85) REVERT: N 23 GLN cc_start: 0.8349 (mt0) cc_final: 0.7705 (tt0) REVERT: P 63 LYS cc_start: 0.7487 (tppt) cc_final: 0.7244 (tptp) REVERT: Q 66 MET cc_start: 0.7618 (mtm) cc_final: 0.7370 (mtt) REVERT: R 81 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7540 (ttpp) REVERT: R 113 GLU cc_start: 0.6961 (tp30) cc_final: 0.6720 (tp30) REVERT: R 213 GLU cc_start: 0.7296 (mp0) cc_final: 0.6730 (pm20) REVERT: S 55 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7311 (ptpt) REVERT: T 3 MET cc_start: 0.9034 (mtp) cc_final: 0.8544 (mtp) REVERT: T 110 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: U 93 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6867 (ttp-110) REVERT: V 29 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7799 (mp) REVERT: V 155 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6704 (mm-30) REVERT: V 401 LYS cc_start: 0.6343 (OUTLIER) cc_final: 0.5960 (pttt) REVERT: W 110 ASN cc_start: 0.8956 (m-40) cc_final: 0.8689 (m-40) REVERT: W 143 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7905 (ttm-80) REVERT: X 176 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7136 (mt0) outliers start: 89 outliers final: 54 residues processed: 702 average time/residue: 1.7706 time to fit residues: 1565.6915 Evaluate side-chains 701 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 629 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 1 residue 138 ASP Chi-restraints excluded: chain 3 residue 158 GLN Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 283 LEU Chi-restraints excluded: chain 4 residue 291 VAL Chi-restraints excluded: chain 4 residue 292 TYR Chi-restraints excluded: chain 4 residue 320 LEU Chi-restraints excluded: chain 4 residue 348 PHE Chi-restraints excluded: chain 4 residue 391 PHE Chi-restraints excluded: chain 4 residue 394 TYR Chi-restraints excluded: chain 4 residue 512 ILE Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 589 THR Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 8 residue 189 VAL Chi-restraints excluded: chain 8 residue 202 SER Chi-restraints excluded: chain 8 residue 363 MET Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 102 ARG Chi-restraints excluded: chain K residue 112 ARG Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain T residue 144 GLU Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 155 GLU Chi-restraints excluded: chain V residue 332 GLU Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain V residue 401 LYS Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 172 ILE Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 176 GLN Chi-restraints excluded: chain X residue 255 MET Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain Y residue 260 ASP Chi-restraints excluded: chain Y residue 349 HIS Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 398 optimal weight: 4.9990 chunk 642 optimal weight: 2.9990 chunk 391 optimal weight: 3.9990 chunk 304 optimal weight: 0.4980 chunk 446 optimal weight: 8.9990 chunk 673 optimal weight: 7.9990 chunk 619 optimal weight: 9.9990 chunk 536 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 414 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 6 170 GLN 6 195 GLN 7 107 GLN F 216 GLN I 141 GLN I 184 ASN L 118 ASN O 65 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2514 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= 0.290 Angle : 0.812 50.569 99390 Z= 0.486 Chirality : 0.123 6.374 11600 Planarity : 0.005 0.118 9592 Dihedral : 19.385 173.557 19547 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 1.67 % Allowed : 15.00 % Favored : 83.33 % 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: 1.33 (0.11), residues: 5969 helix: 1.68 (0.10), residues: 2856 sheet: -0.08 (0.20), residues: 624 loop : 0.34 (0.13), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP 4 313 HIS 0.007 0.001 HIS 7 52 PHE 0.029 0.001 PHE Y 380 TYR 0.022 0.002 TYR C 61 ARG 0.015 0.000 ARG H 75 ********************** 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 726 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 637 time to evaluate : 4.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 196 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8198 (mm) REVERT: 1 269 MET cc_start: 0.8569 (mtp) cc_final: 0.8200 (mtm) REVERT: 3 172 ASP cc_start: 0.8367 (t70) cc_final: 0.8070 (t0) REVERT: 4 530 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: 6 92 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7121 (ttp-110) REVERT: B 58 PHE cc_start: 0.6994 (t80) cc_final: 0.6572 (t80) REVERT: B 102 MET cc_start: 0.9150 (mmm) cc_final: 0.8574 (mmt) REVERT: B 119 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7717 (mm-30) REVERT: D 361 GLN cc_start: 0.8861 (mt0) cc_final: 0.8539 (mt0) REVERT: G 122 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7373 (mtp85) REVERT: G 172 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7694 (mt) REVERT: G 211 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7172 (mt-10) REVERT: G 220 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: H 113 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7611 (ptm-80) REVERT: J 75 SER cc_start: 0.8924 (p) cc_final: 0.8638 (p) REVERT: K 102 ARG cc_start: 0.5235 (OUTLIER) cc_final: 0.4851 (mtm110) REVERT: L 166 MET cc_start: 0.8941 (mtm) cc_final: 0.8602 (mtp) REVERT: L 216 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: L 217 THR cc_start: 0.8626 (m) cc_final: 0.8413 (m) REVERT: M 114 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7735 (mtt-85) REVERT: N 23 GLN cc_start: 0.8352 (mt0) cc_final: 0.7711 (tt0) REVERT: P 63 LYS cc_start: 0.7491 (tppt) cc_final: 0.7218 (tptp) REVERT: Q 66 MET cc_start: 0.7616 (mtm) cc_final: 0.7366 (mtt) REVERT: R 81 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7536 (ttpp) REVERT: R 113 GLU cc_start: 0.6964 (tp30) cc_final: 0.6723 (tp30) REVERT: R 213 GLU cc_start: 0.7302 (mp0) cc_final: 0.6737 (pm20) REVERT: S 55 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7303 (ptpt) REVERT: T 3 MET cc_start: 0.9033 (mtp) cc_final: 0.8546 (mtp) REVERT: T 110 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: U 93 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6864 (ttp-110) REVERT: V 29 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7800 (mp) REVERT: V 155 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6652 (mm-30) REVERT: V 401 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.6051 (pttt) REVERT: W 110 ASN cc_start: 0.8973 (m-40) cc_final: 0.8697 (m-40) REVERT: W 143 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7913 (ttm-80) REVERT: X 100 MET cc_start: 0.9042 (ttm) cc_final: 0.8840 (ttp) REVERT: X 176 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7127 (mt0) outliers start: 89 outliers final: 55 residues processed: 692 average time/residue: 1.7698 time to fit residues: 1545.8629 Evaluate side-chains 704 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 630 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 1 residue 138 ASP Chi-restraints excluded: chain 3 residue 158 GLN Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 157 LEU Chi-restraints excluded: chain 4 residue 266 MET Chi-restraints excluded: chain 4 residue 291 VAL Chi-restraints excluded: chain 4 residue 292 TYR Chi-restraints excluded: chain 4 residue 320 LEU Chi-restraints excluded: chain 4 residue 348 PHE Chi-restraints excluded: chain 4 residue 512 ILE Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 589 THR Chi-restraints excluded: chain 6 residue 92 ARG Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 7 residue 151 THR Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 8 residue 189 VAL Chi-restraints excluded: chain 8 residue 202 SER Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 363 MET Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 184 ASN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 102 ARG Chi-restraints excluded: chain K residue 112 ARG Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain T residue 110 GLU Chi-restraints excluded: chain T residue 144 GLU Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 155 GLU Chi-restraints excluded: chain V residue 332 GLU Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain V residue 401 LYS Chi-restraints excluded: chain W residue 143 ARG Chi-restraints excluded: chain W residue 172 ILE Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 176 GLN Chi-restraints excluded: chain X residue 255 MET Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain Y residue 260 ASP Chi-restraints excluded: chain Y residue 349 HIS Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 676 random chunks: chunk 425 optimal weight: 9.9990 chunk 571 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 494 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 537 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 551 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 6 195 GLN 7 282 GLN F 216 GLN I 141 GLN I 146 HIS I 184 ASN O 65 GLN O 225 GLN Q 79 ASN Q 85 GLN R 278 ASN R 299 ASN R 320 GLN X 73 GLN ** Y 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114066 restraints weight = 103702.852| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.40 r_work: 0.3358 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 70563 Z= 0.275 Angle : 0.803 50.559 99390 Z= 0.482 Chirality : 0.123 6.362 11600 Planarity : 0.004 0.117 9592 Dihedral : 19.360 172.614 19547 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.79 % Favored : 98.19 % Rotamer: Outliers : 1.61 % Allowed : 15.17 % Favored : 83.22 % 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: 1.39 (0.11), residues: 5969 helix: 1.72 (0.10), residues: 2866 sheet: 0.03 (0.21), residues: 609 loop : 0.35 (0.13), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 4 313 HIS 0.007 0.001 HIS 7 52 PHE 0.045 0.001 PHE Y 380 TYR 0.020 0.001 TYR C 61 ARG 0.014 0.000 ARG H 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25822.08 seconds wall clock time: 447 minutes 55.99 seconds (26875.99 seconds total)