Starting phenix.real_space_refine on Tue Feb 20 03:10:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwm_29512/02_2024/8fwm_29512.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwm_29512/02_2024/8fwm_29512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwm_29512/02_2024/8fwm_29512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwm_29512/02_2024/8fwm_29512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwm_29512/02_2024/8fwm_29512.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwm_29512/02_2024/8fwm_29512.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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: 4 Type Number sf(0) Gaussians S 155 5.16 5 C 16783 2.51 5 N 4494 2.21 5 O 5237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 ASP 17": "OD1" <-> "OD2" Residue "3 PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 77": "NH1" <-> "NH2" Residue "3 PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 116": "OE1" <-> "OE2" Residue "3 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 158": "OE1" <-> "OE2" Residue "3 PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 223": "OD1" <-> "OD2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 153": "OD1" <-> "OD2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 178": "OD1" <-> "OD2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 25": "OE1" <-> "OE2" Residue "F PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 178": "OD1" <-> "OD2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 153": "OD1" <-> "OD2" Residue "G PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 24": "OE1" <-> "OE2" Residue "p GLU 31": "OE1" <-> "OE2" Residue "p ASP 37": "OD1" <-> "OD2" Residue "p PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 87": "OE1" <-> "OE2" Residue "p ASP 208": "OD1" <-> "OD2" Residue "p ASP 226": "OD1" <-> "OD2" Residue "p TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 267": "OD1" <-> "OD2" Residue "p GLU 325": "OE1" <-> "OE2" Residue "p PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 377": "NH1" <-> "NH2" Residue "p GLU 400": "OE1" <-> "OE2" Residue "p ASP 449": "OD1" <-> "OD2" Residue "p ASP 454": "OD1" <-> "OD2" Residue "p PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 4": "OD1" <-> "OD2" Residue "q ASP 8": "OD1" <-> "OD2" Residue "q ASP 16": "OD1" <-> "OD2" Residue "q PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 43": "OD1" <-> "OD2" Residue "q ASP 53": "OD1" <-> "OD2" Residue "q ARG 57": "NH1" <-> "NH2" Residue "q PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 87": "OE1" <-> "OE2" Residue "q GLU 215": "OE1" <-> "OE2" Residue "q ASP 226": "OD1" <-> "OD2" Residue "q TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 307": "OE1" <-> "OE2" Residue "q PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 374": "OE1" <-> "OE2" Residue "q PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 400": "OE1" <-> "OE2" Residue "q PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 439": "OD1" <-> "OD2" Residue "q PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 488": "NH1" <-> "NH2" Residue "r PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 37": "OD1" <-> "OD2" Residue "r GLU 66": "OE1" <-> "OE2" Residue "r TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 215": "OE1" <-> "OE2" Residue "r ASP 229": "OD1" <-> "OD2" Residue "r PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 273": "OE1" <-> "OE2" Residue "r TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 307": "OE1" <-> "OE2" Residue "r PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 439": "OD1" <-> "OD2" Residue "r GLU 447": "OE1" <-> "OE2" Residue "r ASP 460": "OD1" <-> "OD2" Residue "r PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 53": "OD1" <-> "OD2" Residue "s GLU 66": "OE1" <-> "OE2" Residue "s ASP 88": "OD1" <-> "OD2" Residue "s ASP 208": "OD1" <-> "OD2" Residue "s TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 215": "OE1" <-> "OE2" Residue "s ASP 226": "OD1" <-> "OD2" Residue "s ASP 229": "OD1" <-> "OD2" Residue "s PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 325": "OE1" <-> "OE2" Residue "s PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 400": "OE1" <-> "OE2" Residue "s PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 453": "OE1" <-> "OE2" Residue "s ASP 454": "OD1" <-> "OD2" Residue "s GLU 462": "OE1" <-> "OE2" Residue "s PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 479": "NH1" <-> "NH2" Residue "s ARG 481": "NH1" <-> "NH2" Residue "s ARG 488": "NH1" <-> "NH2" Residue "AV PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AV ASP 35": "OD1" <-> "OD2" Residue "AV TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AV TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AV GLU 90": "OE1" <-> "OE2" Residue "AV GLU 106": "OE1" <-> "OE2" Residue "AV ASP 125": "OD1" <-> "OD2" Residue "Aa PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa ASP 20": "OD1" <-> "OD2" Residue "Aa ASP 35": "OD1" <-> "OD2" Residue "Aa TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa GLU 109": "OE1" <-> "OE2" Residue "Ae PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae ASP 20": "OD1" <-> "OD2" Residue "Ae GLU 106": "OE1" <-> "OE2" Residue "Ae GLU 109": "OE1" <-> "OE2" Residue "Ae GLU 123": "OE1" <-> "OE2" Residue "Ae GLU 126": "OE1" <-> "OE2" Residue "Ad PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad GLU 90": "OE1" <-> "OE2" Residue "Ad PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad GLU 101": "OE1" <-> "OE2" Residue "AS GLU 15": "OE1" <-> "OE2" Residue "AS GLU 27": "OE1" <-> "OE2" Residue "AS ASP 40": "OD1" <-> "OD2" Residue "AS PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS ARG 92": "NH1" <-> "NH2" Residue "AS ASP 93": "OD1" <-> "OD2" Residue "AS ARG 94": "NH1" <-> "NH2" Residue "AS PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS ASP 106": "OD1" <-> "OD2" Residue "AS TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS ASP 141": "OD1" <-> "OD2" Residue "AS TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS GLU 146": "OE1" <-> "OE2" Residue "AS TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS GLU 161": "OE1" <-> "OE2" Residue "AS GLU 167": "OE1" <-> "OE2" Residue "AS ARG 170": "NH1" <-> "NH2" Residue "AS PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT GLU 15": "OE1" <-> "OE2" Residue "AT PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT GLU 27": "OE1" <-> "OE2" Residue "AT GLU 29": "OE1" <-> "OE2" Residue "AT ASP 40": "OD1" <-> "OD2" Residue "AT ASP 61": "OD1" <-> "OD2" Residue "AT ASP 78": "OD1" <-> "OD2" Residue "AT PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT ARG 92": "NH1" <-> "NH2" Residue "AT ASP 93": "OD1" <-> "OD2" Residue "AT ARG 94": "NH1" <-> "NH2" Residue "AT PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT ASP 106": "OD1" <-> "OD2" Residue "AT PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT ASP 141": "OD1" <-> "OD2" Residue "AT GLU 146": "OE1" <-> "OE2" Residue "AT PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT GLU 161": "OE1" <-> "OE2" Residue "AT GLU 167": "OE1" <-> "OE2" Residue "AT PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26669 Number of models: 1 Model: "" Number of chains: 15 Chain: "3" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1723 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "D" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1723 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1723 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1690 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 206} Chain breaks: 1 Chain: "G" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1723 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 211} Chain: "p" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2842 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 2 Chain: "q" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2871 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 20, 'TRANS': 352} Chain breaks: 2 Chain: "r" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2842 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 2 Chain: "s" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2863 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 20, 'TRANS': 351} Chain breaks: 2 Chain: "AV" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 119} Chain: "Aa" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 119} Chain: "Ae" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 119} Chain: "Ad" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 119} Chain: "AS" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1376 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 164} Chain: "AT" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1385 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 165} Time building chain proxies: 13.33, per 1000 atoms: 0.50 Number of scatterers: 26669 At special positions: 0 Unit cell: (185.76, 154.44, 156.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 155 16.00 O 5237 8.00 N 4494 7.00 C 16783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS 3 19 " - pdb=" SG CYS r 467 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 24 " - pdb=" SG CYS 3 221 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 229 " - pdb=" SG CYS G 23 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS q 244 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS s 467 " distance=2.14 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS F 229 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 221 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS G 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 221 " distance=2.02 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 221 " distance=2.03 Simple disulfide: pdb=" SG CYS p 14 " - pdb=" SG CYS s 244 " distance=2.03 Simple disulfide: pdb=" SG CYS p 26 " - pdb=" SG CYS p 303 " distance=2.03 Simple disulfide: pdb=" SG CYS p 73 " - pdb=" SG CYS p 320 " distance=2.00 Simple disulfide: pdb=" SG CYS p 75 " - pdb=" SG CYS p 300 " distance=2.04 Simple disulfide: pdb=" SG CYS p 217 " - pdb=" SG CYS p 249 " distance=2.02 Simple disulfide: pdb=" SG CYS p 327 " - pdb=" SG CYS r 216 " distance=2.03 Simple disulfide: pdb=" SG CYS q 26 " - pdb=" SG CYS q 303 " distance=2.04 Simple disulfide: pdb=" SG CYS q 73 " - pdb=" SG CYS q 320 " distance=2.03 Simple disulfide: pdb=" SG CYS q 75 " - pdb=" SG CYS q 300 " distance=2.03 Simple disulfide: pdb=" SG CYS q 217 " - pdb=" SG CYS q 249 " distance=2.03 Simple disulfide: pdb=" SG CYS r 26 " - pdb=" SG CYS r 303 " distance=2.02 Simple disulfide: pdb=" SG CYS r 73 " - pdb=" SG CYS r 320 " distance=2.04 Simple disulfide: pdb=" SG CYS r 75 " - pdb=" SG CYS r 300 " distance=2.03 Simple disulfide: pdb=" SG CYS r 217 " - pdb=" SG CYS r 249 " distance=2.02 Simple disulfide: pdb=" SG CYS s 26 " - pdb=" SG CYS s 303 " distance=2.03 Simple disulfide: pdb=" SG CYS s 73 " - pdb=" SG CYS s 320 " distance=2.04 Simple disulfide: pdb=" SG CYS s 75 " - pdb=" SG CYS s 300 " distance=2.03 Simple disulfide: pdb=" SG CYS s 217 " - pdb=" SG CYS s 249 " distance=2.03 Simple disulfide: pdb=" SG CYSAV 43 " - pdb=" SG CYSAa 82 " distance=2.03 Simple disulfide: pdb=" SG CYSAa 19 " - pdb=" SG CYSAe 3 " distance=2.03 Simple disulfide: pdb=" SG CYSAe 43 " - pdb=" SG CYSAd 82 " distance=2.03 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: 9.55 Conformation dependent library (CDL) restraints added in 5.0 seconds 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6378 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 47 sheets defined 17.8% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain '3' and resid 41 through 46 Processing helix chain '3' and resid 105 through 109 removed outlier: 3.693A pdb=" N GLY 3 109 " --> pdb=" O GLU 3 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.976A pdb=" N GLY F 109 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 20 removed outlier: 3.770A pdb=" N CYS G 19 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 Processing helix chain 'G' and resid 106 through 109 Processing helix chain 'p' and resid 62 through 73 removed outlier: 3.702A pdb=" N GLU p 66 " --> pdb=" O SER p 62 " (cutoff:3.500A) Processing helix chain 'p' and resid 227 through 242 Processing helix chain 'p' and resid 260 through 267 Processing helix chain 'p' and resid 286 through 303 removed outlier: 4.136A pdb=" N THR p 290 " --> pdb=" O LEU p 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN p 291 " --> pdb=" O PRO p 287 " (cutoff:3.500A) Processing helix chain 'p' and resid 332 through 343 Processing helix chain 'p' and resid 379 through 383 Processing helix chain 'p' and resid 384 through 403 removed outlier: 3.897A pdb=" N GLN p 403 " --> pdb=" O ALA p 399 " (cutoff:3.500A) Processing helix chain 'p' and resid 404 through 406 No H-bonds generated for 'chain 'p' and resid 404 through 406' Processing helix chain 'p' and resid 425 through 438 Processing helix chain 'p' and resid 450 through 455 removed outlier: 3.777A pdb=" N ILE p 455 " --> pdb=" O ILE p 451 " (cutoff:3.500A) Processing helix chain 'p' and resid 460 through 464 Processing helix chain 'q' and resid 62 through 75 removed outlier: 3.658A pdb=" N CYS q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) Processing helix chain 'q' and resid 208 through 213 removed outlier: 3.538A pdb=" N VAL q 212 " --> pdb=" O ASP q 208 " (cutoff:3.500A) Processing helix chain 'q' and resid 227 through 243 Processing helix chain 'q' and resid 260 through 267 Processing helix chain 'q' and resid 286 through 302 removed outlier: 3.699A pdb=" N THR q 290 " --> pdb=" O LEU q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 332 through 342 removed outlier: 3.670A pdb=" N ALA q 341 " --> pdb=" O THR q 337 " (cutoff:3.500A) Processing helix chain 'q' and resid 384 through 403 Processing helix chain 'q' and resid 425 through 441 Processing helix chain 'q' and resid 450 through 455 removed outlier: 3.519A pdb=" N ILE q 455 " --> pdb=" O ILE q 451 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 removed outlier: 4.590A pdb=" N ILE r 55 " --> pdb=" O LEU r 52 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 75 removed outlier: 4.136A pdb=" N CYS r 75 " --> pdb=" O VAL r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 227 through 241 Processing helix chain 'r' and resid 260 through 267 Processing helix chain 'r' and resid 286 through 302 removed outlier: 4.227A pdb=" N THR r 290 " --> pdb=" O LEU r 286 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN r 291 " --> pdb=" O PRO r 287 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS r 300 " --> pdb=" O ALA r 296 " (cutoff:3.500A) Processing helix chain 'r' and resid 332 through 342 Processing helix chain 'r' and resid 378 through 383 Processing helix chain 'r' and resid 384 through 403 removed outlier: 3.521A pdb=" N ARG r 388 " --> pdb=" O ASP r 384 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN r 403 " --> pdb=" O ALA r 399 " (cutoff:3.500A) Processing helix chain 'r' and resid 404 through 406 No H-bonds generated for 'chain 'r' and resid 404 through 406' Processing helix chain 'r' and resid 425 through 441 Processing helix chain 'r' and resid 450 through 455 removed outlier: 3.620A pdb=" N ILE r 455 " --> pdb=" O ILE r 451 " (cutoff:3.500A) Processing helix chain 'r' and resid 460 through 464 Processing helix chain 's' and resid 62 through 75 Processing helix chain 's' and resid 227 through 239 Processing helix chain 's' and resid 260 through 267 Processing helix chain 's' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR s 290 " --> pdb=" O LEU s 286 " (cutoff:3.500A) Processing helix chain 's' and resid 332 through 342 Processing helix chain 's' and resid 379 through 383 removed outlier: 3.968A pdb=" N PHE s 382 " --> pdb=" O ASN s 379 " (cutoff:3.500A) Processing helix chain 's' and resid 384 through 402 Processing helix chain 's' and resid 425 through 441 removed outlier: 3.849A pdb=" N LYS s 432 " --> pdb=" O LEU s 428 " (cutoff:3.500A) Processing helix chain 's' and resid 450 through 455 removed outlier: 3.580A pdb=" N ASP s 454 " --> pdb=" O ASN s 450 " (cutoff:3.500A) Processing helix chain 's' and resid 459 through 463 removed outlier: 3.650A pdb=" N GLU s 462 " --> pdb=" O THR s 459 " (cutoff:3.500A) Processing helix chain 's' and resid 465 through 469 removed outlier: 4.155A pdb=" N GLY s 469 " --> pdb=" O LYS s 466 " (cutoff:3.500A) Processing helix chain 'AV' and resid 76 through 81 removed outlier: 3.508A pdb=" N GLYAV 81 " --> pdb=" O ALAAV 77 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 75 through 80 Processing helix chain 'Ae' and resid 75 through 79 Processing helix chain 'Ad' and resid 76 through 81 Processing helix chain 'AS' and resid 12 through 20 Processing helix chain 'AS' and resid 25 through 29 removed outlier: 3.961A pdb=" N ILEAS 28 " --> pdb=" O PHEAS 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLUAS 29 " --> pdb=" O HISAS 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'AS' and resid 25 through 29' Processing helix chain 'AS' and resid 107 through 126 Processing helix chain 'AT' and resid 12 through 21 Processing helix chain 'AT' and resid 107 through 126 Processing sheet with id=AA1, first strand: chain '3' and resid 2 through 5 removed outlier: 6.177A pdb=" N TYR 3 2 " --> pdb=" O MET 3 38 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER 3 40 " --> pdb=" O TYR 3 2 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE 3 4 " --> pdb=" O SER 3 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3' and resid 2 through 5 removed outlier: 6.177A pdb=" N TYR 3 2 " --> pdb=" O MET 3 38 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER 3 40 " --> pdb=" O TYR 3 2 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE 3 4 " --> pdb=" O SER 3 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 25 through 29 removed outlier: 6.693A pdb=" N GLU 3 25 " --> pdb=" O ASP 3 223 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER 3 225 " --> pdb=" O GLU 3 25 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE 3 27 " --> pdb=" O SER 3 225 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE 3 216 " --> pdb=" O ALA 3 208 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL 3 199 " --> pdb=" O VAL 3 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 74 through 78 removed outlier: 6.738A pdb=" N ALA 3 74 " --> pdb=" O VAL 3 149 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER 3 151 " --> pdb=" O ALA 3 74 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY 3 76 " --> pdb=" O SER 3 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 84 through 87 Processing sheet with id=AA6, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.265A pdb=" N TYR D 2 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER D 40 " --> pdb=" O TYR D 2 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE D 4 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.265A pdb=" N TYR D 2 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER D 40 " --> pdb=" O TYR D 2 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE D 4 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 25 through 29 removed outlier: 6.462A pdb=" N GLU D 25 " --> pdb=" O ASP D 223 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER D 225 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 27 " --> pdb=" O SER D 225 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 216 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL D 199 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 74 through 79 Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 87 Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AB4, first strand: chain 'E' and resid 25 through 29 Processing sheet with id=AB5, first strand: chain 'E' and resid 74 through 79 removed outlier: 6.451A pdb=" N ALA E 74 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N SER E 151 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY E 76 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASP E 153 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR E 78 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 87 Processing sheet with id=AB7, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.156A pdb=" N TYR F 2 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER F 40 " --> pdb=" O TYR F 2 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE F 4 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.156A pdb=" N TYR F 2 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER F 40 " --> pdb=" O TYR F 2 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE F 4 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 25 through 29 removed outlier: 6.573A pdb=" N GLU F 25 " --> pdb=" O ASP F 223 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER F 225 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE F 27 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL F 199 " --> pdb=" O VAL F 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 84 through 87 Processing sheet with id=AC2, first strand: chain 'F' and resid 133 through 141 Processing sheet with id=AC3, first strand: chain 'G' and resid 2 through 5 Processing sheet with id=AC4, first strand: chain 'G' and resid 2 through 5 Processing sheet with id=AC5, first strand: chain 'G' and resid 25 through 29 removed outlier: 6.484A pdb=" N GLU G 25 " --> pdb=" O ASP G 223 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER G 225 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE G 27 " --> pdb=" O SER G 225 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE G 216 " --> pdb=" O ALA G 208 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL G 199 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 74 through 75 removed outlier: 3.642A pdb=" N ALA G 74 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL G 149 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 84 through 87 Processing sheet with id=AC8, first strand: chain 'p' and resid 82 through 85 removed outlier: 6.673A pdb=" N VAL p 30 " --> pdb=" O LEU p 84 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE p 256 " --> pdb=" O LEU p 223 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU p 277 " --> pdb=" O GLY p 253 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL p 255 " --> pdb=" O LEU p 277 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'p' and resid 456 through 459 Processing sheet with id=AD1, first strand: chain 'p' and resid 489 through 491 removed outlier: 6.451A pdb=" N ASN p 490 " --> pdb=" O LEU r 476 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'q' and resid 46 through 47 removed outlier: 6.602A pdb=" N CYS q 26 " --> pdb=" O SER q 80 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR q 82 " --> pdb=" O CYS q 26 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE q 28 " --> pdb=" O TYR q 82 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU q 84 " --> pdb=" O ILE q 28 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL q 30 " --> pdb=" O LEU q 84 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG q 86 " --> pdb=" O VAL q 30 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY q 32 " --> pdb=" O ARG q 86 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL q 220 " --> pdb=" O GLY q 25 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS q 27 " --> pdb=" O VAL q 220 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL q 222 " --> pdb=" O LYS q 27 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU q 29 " --> pdb=" O VAL q 222 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR q 221 " --> pdb=" O TYR q 254 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N PHE q 256 " --> pdb=" O TYR q 221 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N LEU q 223 " --> pdb=" O PHE q 256 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N LYS q 258 " --> pdb=" O LEU q 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'q' and resid 492 through 494 Processing sheet with id=AD4, first strand: chain 'r' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'r' and resid 46 through 47 removed outlier: 3.543A pdb=" N ALA r 83 " --> pdb=" O THR r 46 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE r 28 " --> pdb=" O TYR r 82 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU r 84 " --> pdb=" O ILE r 28 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL r 30 " --> pdb=" O LEU r 84 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG r 86 " --> pdb=" O VAL r 30 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY r 32 " --> pdb=" O ARG r 86 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR r 221 " --> pdb=" O TYR r 254 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N PHE r 256 " --> pdb=" O TYR r 221 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU r 223 " --> pdb=" O PHE r 256 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LEU r 277 " --> pdb=" O GLY r 253 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL r 255 " --> pdb=" O LEU r 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 's' and resid 79 through 81 removed outlier: 7.105A pdb=" N GLY s 25 " --> pdb=" O SER s 80 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU s 84 " --> pdb=" O ILE s 28 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL s 30 " --> pdb=" O LEU s 84 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG s 86 " --> pdb=" O VAL s 30 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY s 32 " --> pdb=" O ARG s 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 's' and resid 79 through 81 removed outlier: 7.105A pdb=" N GLY s 25 " --> pdb=" O SER s 80 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR s 221 " --> pdb=" O TYR s 254 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N PHE s 256 " --> pdb=" O TYR s 221 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LEU s 223 " --> pdb=" O PHE s 256 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N LYS s 258 " --> pdb=" O LEU s 223 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY s 253 " --> pdb=" O SER s 275 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU s 277 " --> pdb=" O GLY s 253 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL s 255 " --> pdb=" O LEU s 277 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU s 279 " --> pdb=" O VAL s 255 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN s 257 " --> pdb=" O LEU s 279 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 's' and resid 346 through 347 removed outlier: 4.189A pdb=" N VAL s 346 " --> pdb=" O TYR s 364 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR s 364 " --> pdb=" O VAL s 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 's' and resid 409 through 410 removed outlier: 6.869A pdb=" N ALA s 409 " --> pdb=" O THR s 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'AV' and resid 24 through 29 removed outlier: 5.695A pdb=" N ILEAV 14 " --> pdb=" O PROAV 27 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SERAV 29 " --> pdb=" O ILEAV 12 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILEAV 12 " --> pdb=" O SERAV 29 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLUAV 90 " --> pdb=" O LYSAV 10 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILEAV 12 " --> pdb=" O GLNAV 88 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLNAV 88 " --> pdb=" O ILEAV 12 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILEAV 14 " --> pdb=" O ASPAV 86 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASPAV 86 " --> pdb=" O ILEAV 14 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHEAV 16 " --> pdb=" O GLNAV 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLNAV 84 " --> pdb=" O PHEAV 16 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VALAV 85 " --> pdb=" O GLUAV 101 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUAV 101 " --> pdb=" O VALAV 85 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'AV' and resid 47 through 49 Processing sheet with id=AE3, first strand: chain 'Aa' and resid 24 through 30 removed outlier: 5.693A pdb=" N ILEAa 14 " --> pdb=" O PROAa 27 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SERAa 29 " --> pdb=" O ILEAa 12 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILEAa 12 " --> pdb=" O SERAa 29 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VALAa 85 " --> pdb=" O GLUAa 101 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLUAa 101 " --> pdb=" O VALAa 85 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Aa' and resid 24 through 30 removed outlier: 5.693A pdb=" N ILEAa 14 " --> pdb=" O PROAa 27 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SERAa 29 " --> pdb=" O ILEAa 12 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILEAa 12 " --> pdb=" O SERAa 29 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VALAa 85 " --> pdb=" O GLUAa 101 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLUAa 101 " --> pdb=" O VALAa 85 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Aa' and resid 47 through 49 Processing sheet with id=AE6, first strand: chain 'Ae' and resid 24 through 29 removed outlier: 5.674A pdb=" N ILEAe 14 " --> pdb=" O PROAe 27 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SERAe 29 " --> pdb=" O ILEAe 12 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILEAe 12 " --> pdb=" O SERAe 29 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VALAe 85 " --> pdb=" O GLUAe 101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLUAe 101 " --> pdb=" O VALAe 85 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Ae' and resid 45 through 46 Processing sheet with id=AE8, first strand: chain 'Ad' and resid 24 through 29 removed outlier: 5.643A pdb=" N ILEAd 14 " --> pdb=" O PROAd 27 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SERAd 29 " --> pdb=" O ILEAd 12 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILEAd 12 " --> pdb=" O SERAd 29 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLUAd 90 " --> pdb=" O LYSAd 10 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILEAd 12 " --> pdb=" O GLNAd 88 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLNAd 88 " --> pdb=" O ILEAd 12 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILEAd 14 " --> pdb=" O ASPAd 86 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASPAd 86 " --> pdb=" O ILEAd 14 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHEAd 16 " --> pdb=" O GLNAd 84 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLNAd 84 " --> pdb=" O PHEAd 16 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VALAd 87 " --> pdb=" O THRAd 100 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THRAd 100 " --> pdb=" O VALAd 87 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VALAd 89 " --> pdb=" O THRAd 98 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THRAd 98 " --> pdb=" O VALAd 89 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYSAd 91 " --> pdb=" O VALAd 96 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VALAd 96 " --> pdb=" O LYSAd 91 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VALAd 120 " --> pdb=" O ALAAd 103 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Ad' and resid 47 through 49 Processing sheet with id=AF1, first strand: chain 'AS' and resid 32 through 35 removed outlier: 4.148A pdb=" N LEUAS 57 " --> pdb=" O VALAS 35 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VALAS 53 " --> pdb=" O ASNAS 85 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASNAS 85 " --> pdb=" O VALAS 53 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VALAS 55 " --> pdb=" O GLUAS 83 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLUAS 83 " --> pdb=" O VALAS 55 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEUAS 57 " --> pdb=" O ILEAS 81 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILEAS 81 " --> pdb=" O LEUAS 57 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SERAS 133 " --> pdb=" O ARGAS 148 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARGAS 150 " --> pdb=" O PHEAS 131 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHEAS 131 " --> pdb=" O ARGAS 150 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASNAS 152 " --> pdb=" O PHEAS 129 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHEAS 129 " --> pdb=" O ASNAS 152 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHEAS 129 " --> pdb=" O ILEAT 68 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'AT' and resid 32 through 35 removed outlier: 4.250A pdb=" N LEUAT 57 " --> pdb=" O VALAT 35 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VALAT 53 " --> pdb=" O ASNAT 85 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASNAT 85 " --> pdb=" O VALAT 53 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VALAT 55 " --> pdb=" O GLUAT 83 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLUAT 83 " --> pdb=" O VALAT 55 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEUAT 57 " --> pdb=" O ILEAT 81 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILEAT 81 " --> pdb=" O LEUAT 57 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SERAT 133 " --> pdb=" O ARGAT 148 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARGAT 150 " --> pdb=" O PHEAT 131 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHEAT 131 " --> pdb=" O ARGAT 150 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2289 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.73 Time building geometry restraints manager: 10.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7745 1.33 - 1.46: 6919 1.46 - 1.59: 12390 1.59 - 1.71: 0 1.71 - 1.84: 201 Bond restraints: 27255 Sorted by residual: bond pdb=" CA ASN 3 10 " pdb=" C ASN 3 10 " ideal model delta sigma weight residual 1.526 1.474 0.052 1.28e-02 6.10e+03 1.66e+01 bond pdb=" CA LEUAd 127 " pdb=" C LEUAd 127 " ideal model delta sigma weight residual 1.527 1.480 0.048 1.20e-02 6.94e+03 1.58e+01 bond pdb=" CA CYS r 303 " pdb=" C CYS r 303 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.29e-02 6.01e+03 1.14e+01 bond pdb=" CA GLNAV 6 " pdb=" C GLNAV 6 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.23e-02 6.61e+03 1.14e+01 bond pdb=" CA TRPAS 155 " pdb=" C TRPAS 155 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.28e-02 6.10e+03 1.06e+01 ... (remaining 27250 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.35: 709 105.35 - 112.51: 13715 112.51 - 119.66: 8525 119.66 - 126.82: 13867 126.82 - 133.98: 329 Bond angle restraints: 37145 Sorted by residual: angle pdb=" N CYS r 303 " pdb=" CA CYS r 303 " pdb=" C CYS r 303 " ideal model delta sigma weight residual 111.36 99.08 12.28 1.09e+00 8.42e-01 1.27e+02 angle pdb=" N GLY 3 11 " pdb=" CA GLY 3 11 " pdb=" C GLY 3 11 " ideal model delta sigma weight residual 114.61 105.37 9.24 1.49e+00 4.50e-01 3.84e+01 angle pdb=" N LYSAS 95 " pdb=" CA LYSAS 95 " pdb=" C LYSAS 95 " ideal model delta sigma weight residual 110.80 98.19 12.61 2.13e+00 2.20e-01 3.50e+01 angle pdb=" N GLNAV 6 " pdb=" CA GLNAV 6 " pdb=" C GLNAV 6 " ideal model delta sigma weight residual 110.42 118.84 -8.42 1.46e+00 4.69e-01 3.33e+01 angle pdb=" N PHE s 250 " pdb=" CA PHE s 250 " pdb=" C PHE s 250 " ideal model delta sigma weight residual 110.80 122.97 -12.17 2.13e+00 2.20e-01 3.26e+01 ... (remaining 37140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14692 17.98 - 35.97: 1207 35.97 - 53.95: 276 53.95 - 71.93: 66 71.93 - 89.92: 35 Dihedral angle restraints: 16276 sinusoidal: 6329 harmonic: 9947 Sorted by residual: dihedral pdb=" CB CYS p 327 " pdb=" SG CYS p 327 " pdb=" SG CYS r 216 " pdb=" CB CYS r 216 " ideal model delta sinusoidal sigma weight residual -86.00 -175.79 89.79 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS r 73 " pdb=" SG CYS r 73 " pdb=" SG CYS r 320 " pdb=" CB CYS r 320 " ideal model delta sinusoidal sigma weight residual -86.00 -172.29 86.29 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS 3 19 " pdb=" SG CYS 3 19 " pdb=" SG CYS r 467 " pdb=" CB CYS r 467 " ideal model delta sinusoidal sigma weight residual 93.00 177.38 -84.38 1 1.00e+01 1.00e-02 8.66e+01 ... (remaining 16273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3499 0.068 - 0.136: 664 0.136 - 0.204: 26 0.204 - 0.272: 1 0.272 - 0.340: 1 Chirality restraints: 4191 Sorted by residual: chirality pdb=" CB ILE p 54 " pdb=" CA ILE p 54 " pdb=" CG1 ILE p 54 " pdb=" CG2 ILE p 54 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA PHE s 250 " pdb=" N PHE s 250 " pdb=" C PHE s 250 " pdb=" CB PHE s 250 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA CYS r 467 " pdb=" N CYS r 467 " pdb=" C CYS r 467 " pdb=" CB CYS r 467 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 4188 not shown) Planarity restraints: 4931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THRAS 165 " 0.023 2.00e-02 2.50e+03 4.43e-02 1.97e+01 pdb=" C THRAS 165 " -0.077 2.00e-02 2.50e+03 pdb=" O THRAS 165 " 0.029 2.00e-02 2.50e+03 pdb=" N ILEAS 166 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS q 246 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO q 247 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO q 247 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO q 247 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO s 465 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C PRO s 465 " -0.067 2.00e-02 2.50e+03 pdb=" O PRO s 465 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS s 466 " 0.023 2.00e-02 2.50e+03 ... (remaining 4928 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3003 2.74 - 3.28: 27581 3.28 - 3.82: 43060 3.82 - 4.36: 49354 4.36 - 4.90: 84830 Nonbonded interactions: 207828 Sorted by model distance: nonbonded pdb=" OG1 THR q 328 " pdb=" OD1 ASN s 214 " model vdw 2.205 2.440 nonbonded pdb=" O GLY r 59 " pdb=" OG1 THR r 65 " model vdw 2.205 2.440 nonbonded pdb=" ND2 ASN r 257 " pdb=" OD2 ASP r 267 " model vdw 2.216 2.520 nonbonded pdb=" NH1 ARGAS 31 " pdb=" O PROAS 51 " model vdw 2.223 2.520 nonbonded pdb=" O ASPAS 41 " pdb=" OG1 THRAS 45 " model vdw 2.228 2.440 ... (remaining 207823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '3' and (resid 1 through 12 or resid 18 through 230)) selection = (chain 'D' and (resid 1 through 12 or resid 18 through 230)) selection = (chain 'E' and (resid 1 through 12 or resid 18 through 230)) selection = chain 'F' selection = (chain 'G' and (resid 1 through 12 or resid 18 through 230)) } ncs_group { reference = chain 'AS' selection = (chain 'AT' and resid 5 through 175) } ncs_group { reference = chain 'AV' selection = chain 'Aa' selection = chain 'Ad' selection = chain 'Ae' } ncs_group { reference = (chain 'p' and resid 5 through 498) selection = (chain 'q' and (resid 5 through 347 or resid 363 through 498)) selection = (chain 'r' and resid 5 through 498) selection = (chain 's' and (resid 5 through 347 or resid 363 through 498)) } 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.860 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 65.480 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.005 0.053 27255 Z= 0.322 Angle : 0.878 12.606 37145 Z= 0.528 Chirality : 0.049 0.340 4191 Planarity : 0.005 0.109 4931 Dihedral : 14.583 89.917 9799 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 1.16 % Allowed : 13.77 % Favored : 85.07 % Rotamer: Outliers : 2.37 % Allowed : 7.07 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.12), residues: 3435 helix: -2.42 (0.18), residues: 487 sheet: -1.95 (0.15), residues: 1025 loop : -4.08 (0.11), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 242 HIS 0.004 0.001 HIS E 218 PHE 0.025 0.001 PHE r 250 TYR 0.038 0.002 TYR p 370 ARG 0.007 0.001 ARG p 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 921 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 3 56 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8114 (ttpp) REVERT: 3 180 ARG cc_start: 0.7990 (mmp-170) cc_final: 0.7723 (mtt90) REVERT: D 33 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7513 (mm-30) REVERT: D 38 MET cc_start: 0.8148 (mtp) cc_final: 0.7502 (mtp) REVERT: D 135 ASP cc_start: 0.6047 (t0) cc_final: 0.3898 (p0) REVERT: D 148 TYR cc_start: 0.7641 (t80) cc_final: 0.6503 (t80) REVERT: D 150 ILE cc_start: 0.6984 (mt) cc_final: 0.5979 (mt) REVERT: D 185 LYS cc_start: 0.8605 (mttt) cc_final: 0.8246 (mttm) REVERT: D 198 ASP cc_start: 0.7492 (m-30) cc_final: 0.7230 (m-30) REVERT: E 14 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6633 (tmmt) REVERT: E 33 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7382 (pt0) REVERT: E 79 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7194 (mmtt) REVERT: E 103 GLU cc_start: 0.7372 (tt0) cc_final: 0.7086 (tt0) REVERT: E 106 GLU cc_start: 0.7627 (tt0) cc_final: 0.7075 (tm-30) REVERT: E 135 ASP cc_start: 0.6644 (t0) cc_final: 0.6186 (m-30) REVERT: E 178 ASP cc_start: 0.7518 (t70) cc_final: 0.7249 (t0) REVERT: F 25 GLU cc_start: 0.8315 (mp0) cc_final: 0.7613 (mp0) REVERT: F 120 ASN cc_start: 0.7262 (t0) cc_final: 0.6127 (p0) REVERT: F 130 LEU cc_start: 0.7589 (mt) cc_final: 0.7357 (tt) REVERT: G 62 ASP cc_start: 0.7293 (m-30) cc_final: 0.6775 (m-30) REVERT: G 70 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7976 (tttt) REVERT: G 131 PHE cc_start: 0.3329 (t80) cc_final: 0.2202 (t80) REVERT: G 148 TYR cc_start: 0.6957 (t80) cc_final: 0.6657 (t80) REVERT: G 169 TYR cc_start: 0.7879 (p90) cc_final: 0.7592 (p90) REVERT: p 345 VAL cc_start: 0.8145 (t) cc_final: 0.7884 (p) REVERT: p 455 ILE cc_start: 0.9213 (mm) cc_final: 0.8997 (mm) REVERT: p 478 MET cc_start: 0.8221 (mtp) cc_final: 0.7970 (mtp) REVERT: q 16 ASP cc_start: 0.8976 (t0) cc_final: 0.8705 (t0) REVERT: q 457 LEU cc_start: 0.9294 (tt) cc_final: 0.9033 (tt) REVERT: q 473 ILE cc_start: 0.7779 (mm) cc_final: 0.7325 (mm) REVERT: r 258 LYS cc_start: 0.6159 (tttp) cc_final: 0.4686 (ptmt) REVERT: r 375 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6366 (tptm) REVERT: r 467 CYS cc_start: 0.4623 (OUTLIER) cc_final: 0.3518 (m) REVERT: r 480 TYR cc_start: 0.5769 (m-10) cc_final: 0.5021 (m-10) REVERT: r 495 PRO cc_start: 0.8122 (Cg_endo) cc_final: 0.7878 (Cg_exo) REVERT: s 64 LEU cc_start: 0.6838 (pp) cc_final: 0.6625 (pp) REVERT: s 72 PHE cc_start: 0.7652 (m-10) cc_final: 0.7111 (m-80) REVERT: s 311 GLN cc_start: 0.8342 (pt0) cc_final: 0.8043 (pt0) REVERT: s 317 LEU cc_start: 0.7343 (tp) cc_final: 0.6775 (pt) REVERT: s 371 LEU cc_start: 0.9186 (mm) cc_final: 0.8908 (mp) REVERT: s 379 ASN cc_start: 0.8000 (t0) cc_final: 0.7015 (t0) REVERT: s 414 ASN cc_start: 0.8461 (m-40) cc_final: 0.8084 (t0) REVERT: AV 52 ASN cc_start: 0.8719 (t0) cc_final: 0.7702 (t0) REVERT: AV 54 TYR cc_start: 0.8737 (m-80) cc_final: 0.8507 (m-80) REVERT: AV 97 MET cc_start: 0.8011 (mmt) cc_final: 0.7757 (mmt) REVERT: AV 109 GLU cc_start: 0.5846 (tp30) cc_final: 0.5381 (mt-10) REVERT: Aa 93 ASP cc_start: 0.8887 (p0) cc_final: 0.8637 (p0) REVERT: Ae 18 ASP cc_start: 0.8150 (t0) cc_final: 0.7721 (t70) REVERT: Ae 126 GLU cc_start: 0.7067 (tt0) cc_final: 0.6756 (tt0) REVERT: Ad 13 LEU cc_start: 0.9082 (mm) cc_final: 0.8806 (mp) REVERT: Ad 52 ASN cc_start: 0.8875 (t0) cc_final: 0.8609 (t0) REVERT: AS 10 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7665 (ttp80) REVERT: AS 112 ASP cc_start: 0.8137 (m-30) cc_final: 0.7763 (m-30) REVERT: AT 18 LYS cc_start: 0.8625 (ptmt) cc_final: 0.8318 (ptmm) REVERT: AT 104 TYR cc_start: 0.8691 (t80) cc_final: 0.5712 (m-80) REVERT: AT 108 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8474 (mt-10) REVERT: AT 112 ASP cc_start: 0.8414 (m-30) cc_final: 0.8144 (m-30) outliers start: 70 outliers final: 19 residues processed: 963 average time/residue: 0.4056 time to fit residues: 589.1981 Evaluate side-chains 605 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 583 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 221 CYS Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 320 CYS Chi-restraints excluded: chain r residue 301 SER Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain s residue 217 CYS Chi-restraints excluded: chain s residue 250 PHE Chi-restraints excluded: chain AS residue 156 CYS Chi-restraints excluded: chain AS residue 157 GLU Chi-restraints excluded: chain AS residue 167 GLU Chi-restraints excluded: chain AS residue 170 ARG Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 158 THR Chi-restraints excluded: chain AT residue 167 GLU Chi-restraints excluded: chain AT residue 170 ARG Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 7.9990 chunk 259 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 310 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 120 ASN F 182 HIS G 55 ASN G 112 ASN p 33 GLN p 365 ASN p 452 ASN q 60 GLN q 263 GLN ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 369 ASN ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 33 GLN r 214 ASN r 252 HIS ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 452 ASN r 475 HIS r 490 ASN s 33 GLN ** s 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 369 ASN s 456 GLN ** s 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN AV 22 GLN ** AV 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 32 GLN Ae 88 GLN AS 46 GLN AT 125 HIS AT 151 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.004 0.080 27255 Z= 0.261 Angle : 0.721 10.478 37145 Z= 0.369 Chirality : 0.047 0.191 4191 Planarity : 0.005 0.104 4931 Dihedral : 6.863 86.270 3786 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.88 % Favored : 87.83 % Rotamer: Outliers : 4.20 % Allowed : 16.31 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.13), residues: 3435 helix: -0.34 (0.22), residues: 525 sheet: -1.43 (0.15), residues: 1040 loop : -3.48 (0.12), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP q 242 HIS 0.004 0.001 HISAT 125 PHE 0.023 0.001 PHE s 58 TYR 0.018 0.002 TYR E 169 ARG 0.011 0.001 ARG s 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 608 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 3 56 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8252 (ttmm) REVERT: 3 180 ARG cc_start: 0.7933 (mmp-170) cc_final: 0.7699 (mtt90) REVERT: D 33 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7646 (mm-30) REVERT: D 67 THR cc_start: 0.8095 (m) cc_final: 0.7838 (p) REVERT: D 159 LEU cc_start: 0.7559 (tp) cc_final: 0.6962 (mp) REVERT: D 185 LYS cc_start: 0.8588 (mttt) cc_final: 0.8274 (mttm) REVERT: E 14 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.6933 (tmmt) REVERT: E 38 MET cc_start: 0.8541 (mtp) cc_final: 0.7795 (mtp) REVERT: E 79 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7192 (mmtt) REVERT: E 135 ASP cc_start: 0.6825 (t0) cc_final: 0.6099 (m-30) REVERT: E 178 ASP cc_start: 0.7549 (t70) cc_final: 0.7259 (t0) REVERT: E 215 GLU cc_start: 0.7749 (mp0) cc_final: 0.7458 (mp0) REVERT: F 1 MET cc_start: 0.8060 (ttt) cc_final: 0.7624 (ttt) REVERT: F 120 ASN cc_start: 0.7357 (t0) cc_final: 0.6187 (p0) REVERT: F 130 LEU cc_start: 0.7667 (mt) cc_final: 0.7338 (tt) REVERT: G 30 ARG cc_start: 0.8073 (ttt-90) cc_final: 0.7364 (mtt-85) REVERT: G 70 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8094 (tttt) REVERT: G 84 PHE cc_start: 0.6755 (t80) cc_final: 0.5999 (t80) REVERT: G 148 TYR cc_start: 0.7135 (t80) cc_final: 0.6480 (t80) REVERT: G 159 LEU cc_start: 0.6670 (mm) cc_final: 0.5984 (mp) REVERT: G 185 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7917 (ptmm) REVERT: p 13 LEU cc_start: 0.8218 (pt) cc_final: 0.7719 (pt) REVERT: q 16 ASP cc_start: 0.8962 (t0) cc_final: 0.8728 (t0) REVERT: q 457 LEU cc_start: 0.9304 (tt) cc_final: 0.9056 (tt) REVERT: r 82 TYR cc_start: 0.7569 (m-80) cc_final: 0.7135 (m-80) REVERT: r 258 LYS cc_start: 0.5967 (tttp) cc_final: 0.4754 (ptmt) REVERT: r 310 ILE cc_start: 0.8298 (mt) cc_final: 0.7940 (mm) REVERT: r 367 VAL cc_start: 0.8637 (m) cc_final: 0.8326 (m) REVERT: r 375 LYS cc_start: 0.7310 (tptm) cc_final: 0.6462 (tmtt) REVERT: r 390 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7842 (tp) REVERT: s 29 LEU cc_start: 0.8493 (tp) cc_final: 0.8246 (tp) REVERT: s 72 PHE cc_start: 0.7855 (m-10) cc_final: 0.7221 (m-80) REVERT: s 317 LEU cc_start: 0.7275 (tp) cc_final: 0.6786 (pt) REVERT: s 379 ASN cc_start: 0.7509 (t0) cc_final: 0.7021 (t0) REVERT: s 414 ASN cc_start: 0.8425 (m-40) cc_final: 0.8087 (t0) REVERT: s 447 GLU cc_start: 0.8330 (tp30) cc_final: 0.8122 (tp30) REVERT: s 460 ASP cc_start: 0.7815 (t0) cc_final: 0.7586 (t0) REVERT: AV 54 TYR cc_start: 0.8697 (m-80) cc_final: 0.8275 (m-80) REVERT: Aa 32 GLN cc_start: 0.8451 (mm110) cc_final: 0.8225 (mm-40) REVERT: Aa 93 ASP cc_start: 0.8868 (p0) cc_final: 0.8648 (p0) REVERT: Ae 18 ASP cc_start: 0.8200 (t0) cc_final: 0.7740 (t0) REVERT: Ad 13 LEU cc_start: 0.9072 (mm) cc_final: 0.8821 (mp) REVERT: Ad 22 GLN cc_start: 0.8595 (mp10) cc_final: 0.8354 (mp10) REVERT: Ad 52 ASN cc_start: 0.8949 (t0) cc_final: 0.8722 (t0) REVERT: Ad 117 MET cc_start: 0.9214 (mtp) cc_final: 0.8955 (mtp) REVERT: AS 10 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7614 (ttp80) REVERT: AS 112 ASP cc_start: 0.8100 (m-30) cc_final: 0.7898 (m-30) REVERT: AT 18 LYS cc_start: 0.8428 (ptmt) cc_final: 0.8142 (ptmm) REVERT: AT 104 TYR cc_start: 0.8771 (t80) cc_final: 0.5897 (m-80) REVERT: AT 108 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8380 (mt-10) outliers start: 124 outliers final: 82 residues processed: 685 average time/residue: 0.3859 time to fit residues: 409.7471 Evaluate side-chains 602 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 518 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 229 CYS Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 320 CYS Chi-restraints excluded: chain p residue 401 PHE Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 453 GLU Chi-restraints excluded: chain q residue 28 ILE Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 26 CYS Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 301 SER Chi-restraints excluded: chain r residue 309 ASN Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 476 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 226 ASP Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Ad residue 6 GLN Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 93 ASP Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 38 VAL Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 124 GLU Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 156 CYS Chi-restraints excluded: chain AS residue 157 GLU Chi-restraints excluded: chain AS residue 167 GLU Chi-restraints excluded: chain AT residue 5 LEU Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 158 THR Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 311 optimal weight: 9.9990 chunk 336 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 106 optimal weight: 0.0070 chunk 249 optimal weight: 2.9990 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN D 214 ASN F 51 HIS ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN r 263 GLN ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 311 GLN s 440 ASN ** s 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 475 HIS AV 6 GLN AV 22 GLN ** AV 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 6 GLN Ae 22 GLN Ae 42 ASN Ae 88 GLN AS 46 GLN AT 151 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27255 Z= 0.371 Angle : 0.721 12.249 37145 Z= 0.371 Chirality : 0.048 0.215 4191 Planarity : 0.006 0.115 4931 Dihedral : 6.313 84.778 3765 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.04 % Favored : 86.67 % Rotamer: Outliers : 6.23 % Allowed : 19.59 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.14), residues: 3435 helix: 0.47 (0.23), residues: 520 sheet: -1.10 (0.16), residues: 969 loop : -3.21 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP q 242 HIS 0.006 0.001 HIS s 252 PHE 0.020 0.002 PHE r 250 TYR 0.024 0.002 TYR s 480 ARG 0.006 0.001 ARG r 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 511 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 30 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.8064 (ttm-80) REVERT: 3 180 ARG cc_start: 0.7973 (mmp-170) cc_final: 0.7701 (mtt90) REVERT: D 33 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7671 (mm-30) REVERT: D 90 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6478 (t70) REVERT: D 185 LYS cc_start: 0.8495 (mttt) cc_final: 0.8193 (mttm) REVERT: D 200 TYR cc_start: 0.8646 (m-80) cc_final: 0.8409 (m-80) REVERT: E 14 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6770 (tmmt) REVERT: E 38 MET cc_start: 0.8553 (mtp) cc_final: 0.7933 (mtp) REVERT: E 135 ASP cc_start: 0.6922 (t0) cc_final: 0.6038 (m-30) REVERT: E 178 ASP cc_start: 0.7665 (t0) cc_final: 0.7442 (t0) REVERT: F 120 ASN cc_start: 0.7714 (t0) cc_final: 0.6230 (p0) REVERT: F 130 LEU cc_start: 0.7617 (mt) cc_final: 0.7382 (tt) REVERT: G 30 ARG cc_start: 0.8182 (ttt-90) cc_final: 0.7788 (ttt-90) REVERT: G 38 MET cc_start: 0.7910 (mtt) cc_final: 0.7469 (mtm) REVERT: G 148 TYR cc_start: 0.6979 (t80) cc_final: 0.6417 (t80) REVERT: G 159 LEU cc_start: 0.6571 (mm) cc_final: 0.6064 (mp) REVERT: G 185 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7956 (ptmm) REVERT: p 58 PHE cc_start: 0.3784 (p90) cc_final: 0.3565 (p90) REVERT: p 370 TYR cc_start: 0.8131 (t80) cc_final: 0.7736 (t80) REVERT: p 460 ASP cc_start: 0.8052 (t0) cc_final: 0.7763 (p0) REVERT: q 16 ASP cc_start: 0.8985 (t0) cc_final: 0.8676 (t0) REVERT: q 450 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7985 (t0) REVERT: r 248 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8233 (pm20) REVERT: r 258 LYS cc_start: 0.5847 (tttp) cc_final: 0.4303 (ptmt) REVERT: r 331 TRP cc_start: 0.6034 (OUTLIER) cc_final: 0.5792 (p90) REVERT: r 375 LYS cc_start: 0.7498 (tptm) cc_final: 0.6460 (tttt) REVERT: r 400 GLU cc_start: 0.8068 (pt0) cc_final: 0.7803 (tm-30) REVERT: r 467 CYS cc_start: 0.4001 (OUTLIER) cc_final: 0.3379 (m) REVERT: s 27 LYS cc_start: 0.7713 (tppt) cc_final: 0.7237 (mmmt) REVERT: s 29 LEU cc_start: 0.8491 (tp) cc_final: 0.8251 (tp) REVERT: s 317 LEU cc_start: 0.7436 (tp) cc_final: 0.6958 (pt) REVERT: s 379 ASN cc_start: 0.7795 (t0) cc_final: 0.7226 (t0) REVERT: s 414 ASN cc_start: 0.8417 (m-40) cc_final: 0.8135 (t0) REVERT: s 447 GLU cc_start: 0.8331 (tp30) cc_final: 0.8123 (tp30) REVERT: AV 54 TYR cc_start: 0.8743 (m-80) cc_final: 0.8303 (m-80) REVERT: Ae 18 ASP cc_start: 0.8366 (t0) cc_final: 0.7902 (t70) REVERT: Ae 97 MET cc_start: 0.8403 (mmt) cc_final: 0.7904 (mmt) REVERT: Ae 101 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8171 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9199 (mm) cc_final: 0.8947 (mp) REVERT: Ad 22 GLN cc_start: 0.8733 (mp10) cc_final: 0.8520 (mp10) REVERT: Ad 52 ASN cc_start: 0.9111 (t0) cc_final: 0.8652 (t0) REVERT: AS 108 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6806 (mm-30) REVERT: AS 112 ASP cc_start: 0.8409 (m-30) cc_final: 0.8037 (m-30) REVERT: AT 94 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8264 (mpp80) REVERT: AT 104 TYR cc_start: 0.8849 (t80) cc_final: 0.5861 (m-10) REVERT: AT 135 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8199 (m-30) outliers start: 184 outliers final: 115 residues processed: 636 average time/residue: 0.3744 time to fit residues: 373.7859 Evaluate side-chains 594 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 472 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 290 THR Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 400 GLU Chi-restraints excluded: chain p residue 401 PHE Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 459 THR Chi-restraints excluded: chain q residue 28 ILE Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 384 ASP Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain q residue 452 ASN Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 228 THR Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 309 ASN Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 226 ASP Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain s residue 440 ASN Chi-restraints excluded: chain AV residue 86 ASP Chi-restraints excluded: chain AV residue 93 ASP Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 86 ASP Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 128 LEU Chi-restraints excluded: chain Ae residue 43 CYS Chi-restraints excluded: chain Ae residue 86 ASP Chi-restraints excluded: chain Ae residue 105 VAL Chi-restraints excluded: chain Ad residue 6 GLN Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 93 ASP Chi-restraints excluded: chain Ad residue 125 ASP Chi-restraints excluded: chain AS residue 13 LEU Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 124 GLU Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 156 CYS Chi-restraints excluded: chain AS residue 157 GLU Chi-restraints excluded: chain AS residue 167 GLU Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 135 ASP Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 148 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 312 optimal weight: 5.9990 chunk 330 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 295 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 490 ASN r 214 ASN ** r 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 365 ASN ** s 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 311 GLN ** s 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN AV 22 GLN ** AV 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 88 GLN Ae 88 GLN AS 46 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27255 Z= 0.282 Angle : 0.674 14.218 37145 Z= 0.341 Chirality : 0.047 0.184 4191 Planarity : 0.005 0.117 4931 Dihedral : 6.044 79.679 3761 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.79 % Favored : 87.92 % Rotamer: Outliers : 5.89 % Allowed : 21.42 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.14), residues: 3435 helix: 0.73 (0.24), residues: 526 sheet: -0.98 (0.16), residues: 1009 loop : -2.96 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP r 331 HIS 0.004 0.001 HIS s 252 PHE 0.020 0.001 PHE G 131 TYR 0.025 0.002 TYR p 480 ARG 0.006 0.000 ARGAS 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 502 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 30 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8020 (ttm-80) REVERT: 3 180 ARG cc_start: 0.7974 (mmp-170) cc_final: 0.7706 (mtt90) REVERT: D 33 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7652 (mm-30) REVERT: D 60 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6763 (tm-30) REVERT: D 201 ARG cc_start: 0.8361 (ttm110) cc_final: 0.7972 (mtp-110) REVERT: E 14 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6340 (tmmt) REVERT: E 135 ASP cc_start: 0.6950 (t0) cc_final: 0.5844 (m-30) REVERT: F 73 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7492 (p0) REVERT: F 120 ASN cc_start: 0.7767 (t0) cc_final: 0.6286 (p0) REVERT: F 226 ILE cc_start: 0.9081 (mm) cc_final: 0.8640 (mt) REVERT: G 30 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7597 (mtt-85) REVERT: G 38 MET cc_start: 0.7896 (mtt) cc_final: 0.7554 (mtm) REVERT: G 62 ASP cc_start: 0.8368 (m-30) cc_final: 0.8164 (m-30) REVERT: G 159 LEU cc_start: 0.6515 (mm) cc_final: 0.5972 (mp) REVERT: G 185 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7930 (ptmm) REVERT: G 206 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8163 (tm-30) REVERT: p 58 PHE cc_start: 0.3719 (p90) cc_final: 0.3303 (p90) REVERT: p 370 TYR cc_start: 0.8120 (t80) cc_final: 0.7762 (t80) REVERT: p 403 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7772 (mm-40) REVERT: p 459 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8009 (t) REVERT: p 460 ASP cc_start: 0.8165 (t0) cc_final: 0.7871 (p0) REVERT: q 16 ASP cc_start: 0.8979 (t0) cc_final: 0.8697 (t0) REVERT: q 450 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7828 (t0) REVERT: q 452 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8074 (p0) REVERT: q 454 ASP cc_start: 0.8663 (m-30) cc_final: 0.8438 (m-30) REVERT: r 22 PHE cc_start: 0.6148 (p90) cc_final: 0.5799 (p90) REVERT: r 82 TYR cc_start: 0.7322 (m-80) cc_final: 0.6603 (m-80) REVERT: r 258 LYS cc_start: 0.5475 (tttp) cc_final: 0.4134 (ptmt) REVERT: r 331 TRP cc_start: 0.5898 (OUTLIER) cc_final: 0.5655 (p90) REVERT: r 365 ASN cc_start: 0.6737 (OUTLIER) cc_final: 0.6430 (p0) REVERT: r 375 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.6614 (tttt) REVERT: r 467 CYS cc_start: 0.3793 (OUTLIER) cc_final: 0.3230 (m) REVERT: s 27 LYS cc_start: 0.7776 (tppt) cc_final: 0.7422 (mmmt) REVERT: s 29 LEU cc_start: 0.8484 (tp) cc_final: 0.8238 (tp) REVERT: s 66 GLU cc_start: 0.8339 (tp30) cc_final: 0.8118 (tp30) REVERT: s 317 LEU cc_start: 0.7471 (tp) cc_final: 0.7091 (pt) REVERT: s 379 ASN cc_start: 0.7741 (t0) cc_final: 0.7246 (t0) REVERT: s 414 ASN cc_start: 0.8408 (m-40) cc_final: 0.8100 (t0) REVERT: s 458 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8757 (mt) REVERT: AV 54 TYR cc_start: 0.8746 (m-80) cc_final: 0.8328 (m-80) REVERT: Aa 126 GLU cc_start: 0.7623 (tt0) cc_final: 0.7368 (tt0) REVERT: Ae 18 ASP cc_start: 0.8404 (t0) cc_final: 0.7922 (t70) REVERT: Ae 97 MET cc_start: 0.8523 (mmt) cc_final: 0.8137 (mmt) REVERT: Ae 101 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7962 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9128 (mm) cc_final: 0.8909 (mp) REVERT: Ad 52 ASN cc_start: 0.9105 (t0) cc_final: 0.8714 (t0) REVERT: AS 106 ASP cc_start: 0.8941 (p0) cc_final: 0.8720 (p0) REVERT: AS 112 ASP cc_start: 0.8386 (m-30) cc_final: 0.8024 (m-30) REVERT: AT 94 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8358 (mpp80) REVERT: AT 104 TYR cc_start: 0.8688 (t80) cc_final: 0.5909 (m-10) outliers start: 174 outliers final: 128 residues processed: 617 average time/residue: 0.3934 time to fit residues: 380.5129 Evaluate side-chains 614 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 476 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 108 ASN Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 400 GLU Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 410 VAL Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 459 THR Chi-restraints excluded: chain p residue 476 LEU Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain q residue 452 ASN Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 214 ASN Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 301 SER Chi-restraints excluded: chain r residue 309 ASN Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 365 ASN Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 226 ASP Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 314 THR Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain AV residue 93 ASP Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 86 ASP Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 128 LEU Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 86 ASP Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 93 ASP Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 125 ASP Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 57 LEU Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 124 GLU Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 157 GLU Chi-restraints excluded: chain AS residue 165 THR Chi-restraints excluded: chain AS residue 167 GLU Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 85 ASN Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 246 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 282 optimal weight: 0.9980 chunk 228 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 365 ASN ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 214 ASN s 342 ASN ** s 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN ** AV 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 88 GLN Ae 22 GLN Ae 88 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 27255 Z= 0.364 Angle : 0.704 12.652 37145 Z= 0.356 Chirality : 0.047 0.179 4191 Planarity : 0.005 0.119 4931 Dihedral : 6.078 77.845 3760 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.63 % Favored : 87.10 % Rotamer: Outliers : 6.40 % Allowed : 22.67 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.14), residues: 3435 helix: 0.87 (0.24), residues: 513 sheet: -0.89 (0.16), residues: 1013 loop : -2.90 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP r 331 HIS 0.005 0.001 HIS F 182 PHE 0.014 0.001 PHE D 186 TYR 0.022 0.002 TYR s 480 ARG 0.009 0.001 ARG p 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 466 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 19 CYS cc_start: 0.4908 (OUTLIER) cc_final: 0.4425 (p) REVERT: 3 30 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8090 (ttt90) REVERT: 3 180 ARG cc_start: 0.7950 (mmp-170) cc_final: 0.7726 (mtt90) REVERT: 3 215 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7411 (mt-10) REVERT: D 33 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7640 (mm-30) REVERT: D 60 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6846 (tm-30) REVERT: D 90 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6521 (t70) REVERT: D 200 TYR cc_start: 0.8763 (m-80) cc_final: 0.8424 (m-80) REVERT: D 201 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8057 (mtp-110) REVERT: E 2 TYR cc_start: 0.7999 (m-80) cc_final: 0.7648 (m-80) REVERT: E 14 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6331 (tmmt) REVERT: E 79 LYS cc_start: 0.7717 (mmmt) cc_final: 0.7398 (mmtt) REVERT: F 1 MET cc_start: 0.7773 (ttt) cc_final: 0.7151 (ttt) REVERT: F 73 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7525 (p0) REVERT: F 226 ILE cc_start: 0.9075 (mm) cc_final: 0.8705 (mt) REVERT: G 62 ASP cc_start: 0.8431 (m-30) cc_final: 0.8221 (m-30) REVERT: G 148 TYR cc_start: 0.7047 (t80) cc_final: 0.6554 (t80) REVERT: G 159 LEU cc_start: 0.6437 (mm) cc_final: 0.5921 (mp) REVERT: G 206 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8045 (tm-30) REVERT: p 58 PHE cc_start: 0.4044 (p90) cc_final: 0.3664 (p90) REVERT: p 265 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8285 (tt) REVERT: p 403 GLN cc_start: 0.8501 (mm-40) cc_final: 0.7611 (mm-40) REVERT: q 16 ASP cc_start: 0.8984 (t0) cc_final: 0.8640 (t0) REVERT: q 372 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7611 (ptp90) REVERT: q 450 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7806 (t0) REVERT: q 452 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8135 (p0) REVERT: q 454 ASP cc_start: 0.8707 (m-30) cc_final: 0.8443 (m-30) REVERT: r 22 PHE cc_start: 0.6269 (p90) cc_final: 0.5894 (p90) REVERT: r 82 TYR cc_start: 0.7356 (m-80) cc_final: 0.6634 (m-80) REVERT: r 258 LYS cc_start: 0.5899 (tttp) cc_final: 0.4406 (ptmt) REVERT: r 331 TRP cc_start: 0.5944 (OUTLIER) cc_final: 0.5634 (p90) REVERT: r 375 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6544 (tttt) REVERT: s 29 LEU cc_start: 0.8490 (tp) cc_final: 0.8260 (tp) REVERT: s 66 GLU cc_start: 0.8334 (tp30) cc_final: 0.8089 (tp30) REVERT: s 317 LEU cc_start: 0.7334 (tp) cc_final: 0.7065 (pt) REVERT: s 379 ASN cc_start: 0.7919 (t0) cc_final: 0.7321 (t0) REVERT: s 414 ASN cc_start: 0.8405 (m-40) cc_final: 0.8115 (t0) REVERT: AV 54 TYR cc_start: 0.8762 (m-80) cc_final: 0.8344 (m-80) REVERT: Aa 126 GLU cc_start: 0.7673 (tt0) cc_final: 0.7404 (tt0) REVERT: Ae 18 ASP cc_start: 0.8411 (t0) cc_final: 0.7938 (t70) REVERT: Ae 101 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7947 (mm-30) REVERT: Ad 13 LEU cc_start: 0.9177 (mm) cc_final: 0.8941 (mp) REVERT: Ad 52 ASN cc_start: 0.9148 (t0) cc_final: 0.8741 (t0) REVERT: AS 112 ASP cc_start: 0.8486 (m-30) cc_final: 0.8073 (m-30) REVERT: AT 104 TYR cc_start: 0.8759 (t80) cc_final: 0.5925 (m-10) REVERT: AT 144 TYR cc_start: 0.8882 (m-80) cc_final: 0.8489 (m-80) outliers start: 189 outliers final: 143 residues processed: 603 average time/residue: 0.3870 time to fit residues: 364.9928 Evaluate side-chains 612 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 459 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 108 ASN Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 290 THR Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 314 THR Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 400 GLU Chi-restraints excluded: chain p residue 408 LEU Chi-restraints excluded: chain p residue 410 VAL Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 372 ARG Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain q residue 452 ASN Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 37 ASP Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 208 ASP Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 228 THR Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 309 ASN Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 226 ASP Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain AV residue 86 ASP Chi-restraints excluded: chain AV residue 93 ASP Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 86 ASP Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Aa residue 128 LEU Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 86 ASP Chi-restraints excluded: chain Ad residue 6 GLN Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 93 ASP Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 125 ASP Chi-restraints excluded: chain AS residue 13 LEU Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 28 ILE Chi-restraints excluded: chain AS residue 35 VAL Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 124 GLU Chi-restraints excluded: chain AS residue 136 ILE Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 157 GLU Chi-restraints excluded: chain AS residue 165 THR Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 85 ASN Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 9.9990 chunk 297 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 342 ASN s 470 GLN AV 6 GLN AV 32 GLN AV 88 GLN Ad 88 GLN AT 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 27255 Z= 0.426 Angle : 0.740 12.484 37145 Z= 0.376 Chirality : 0.049 0.207 4191 Planarity : 0.006 0.121 4931 Dihedral : 6.169 75.916 3757 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.90 % Favored : 86.84 % Rotamer: Outliers : 7.07 % Allowed : 23.18 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.14), residues: 3435 helix: 0.58 (0.23), residues: 533 sheet: -0.86 (0.16), residues: 1018 loop : -2.89 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP r 331 HIS 0.006 0.001 HIS F 182 PHE 0.015 0.002 PHE 3 84 TYR 0.020 0.002 TYR F 222 ARG 0.009 0.001 ARG p 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 466 time to evaluate : 2.908 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: 3 30 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8048 (ttt90) REVERT: 3 180 ARG cc_start: 0.7953 (mmp-170) cc_final: 0.7702 (mtt90) REVERT: 3 215 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7445 (mt-10) REVERT: D 33 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7733 (mm-30) REVERT: D 60 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6775 (tm-30) REVERT: D 73 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7387 (m-40) REVERT: D 90 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6554 (t70) REVERT: D 201 ARG cc_start: 0.8574 (ttm110) cc_final: 0.8186 (mtp-110) REVERT: E 14 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6243 (tmmt) REVERT: E 38 MET cc_start: 0.8620 (mtp) cc_final: 0.7693 (mtp) REVERT: E 79 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7631 (mmtm) REVERT: F 1 MET cc_start: 0.7965 (ttt) cc_final: 0.7608 (ttt) REVERT: F 73 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7587 (p0) REVERT: F 217 VAL cc_start: 0.9078 (t) cc_final: 0.8611 (p) REVERT: G 17 ASP cc_start: 0.8554 (t0) cc_final: 0.8331 (t0) REVERT: G 38 MET cc_start: 0.8027 (mtt) cc_final: 0.7805 (mtt) REVERT: G 148 TYR cc_start: 0.6954 (t80) cc_final: 0.6711 (t80) REVERT: G 159 LEU cc_start: 0.6603 (mm) cc_final: 0.6035 (mp) REVERT: p 58 PHE cc_start: 0.3564 (p90) cc_final: 0.2885 (p90) REVERT: p 403 GLN cc_start: 0.8685 (mm-40) cc_final: 0.7773 (mm-40) REVERT: p 466 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8052 (pttp) REVERT: q 16 ASP cc_start: 0.8987 (t0) cc_final: 0.8637 (t0) REVERT: q 377 ARG cc_start: 0.8293 (mmt-90) cc_final: 0.8006 (mmm-85) REVERT: q 450 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7852 (t0) REVERT: q 454 ASP cc_start: 0.8742 (m-30) cc_final: 0.8479 (m-30) REVERT: r 82 TYR cc_start: 0.7423 (m-80) cc_final: 0.6994 (m-80) REVERT: r 207 ASN cc_start: 0.8288 (p0) cc_final: 0.7679 (p0) REVERT: r 258 LYS cc_start: 0.6119 (tttp) cc_final: 0.4438 (ptmt) REVERT: r 331 TRP cc_start: 0.5779 (OUTLIER) cc_final: 0.5507 (p90) REVERT: r 375 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6385 (tttt) REVERT: r 467 CYS cc_start: 0.3753 (OUTLIER) cc_final: 0.3337 (m) REVERT: s 29 LEU cc_start: 0.8475 (tp) cc_final: 0.8212 (tp) REVERT: s 66 GLU cc_start: 0.8360 (tp30) cc_final: 0.8105 (tp30) REVERT: s 317 LEU cc_start: 0.7348 (tp) cc_final: 0.7064 (pt) REVERT: s 364 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7486 (p90) REVERT: s 379 ASN cc_start: 0.7904 (t0) cc_final: 0.7593 (t0) REVERT: s 414 ASN cc_start: 0.8448 (m-40) cc_final: 0.8155 (t0) REVERT: s 458 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8792 (mt) REVERT: s 461 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8338 (p90) REVERT: AV 54 TYR cc_start: 0.8789 (m-80) cc_final: 0.8362 (m-80) REVERT: Aa 126 GLU cc_start: 0.7955 (tt0) cc_final: 0.7733 (tt0) REVERT: Ae 18 ASP cc_start: 0.8428 (t0) cc_final: 0.7992 (t70) REVERT: Ae 97 MET cc_start: 0.8617 (mmt) cc_final: 0.8267 (mmt) REVERT: Ad 52 ASN cc_start: 0.9102 (t0) cc_final: 0.8721 (t0) REVERT: Ad 117 MET cc_start: 0.8887 (mtp) cc_final: 0.8536 (mtt) REVERT: AT 104 TYR cc_start: 0.8844 (t80) cc_final: 0.5965 (m-10) REVERT: AT 144 TYR cc_start: 0.8869 (m-80) cc_final: 0.8502 (m-80) outliers start: 209 outliers final: 161 residues processed: 618 average time/residue: 0.3681 time to fit residues: 358.4110 Evaluate side-chains 603 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 430 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 108 ASN Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 214 ASN Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 285 VAL Chi-restraints excluded: chain p residue 290 THR Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 410 VAL Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 466 LYS Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 371 LEU Chi-restraints excluded: chain q residue 384 ASP Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 424 THR Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain r residue 11 VAL Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 37 ASP Chi-restraints excluded: chain r residue 39 SER Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 208 ASP Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 309 ASN Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 447 GLU Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 226 ASP Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 364 TYR Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain s residue 461 PHE Chi-restraints excluded: chain s residue 477 ASN Chi-restraints excluded: chain AV residue 40 TYR Chi-restraints excluded: chain AV residue 86 ASP Chi-restraints excluded: chain AV residue 93 ASP Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 25 ILE Chi-restraints excluded: chain Aa residue 43 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 86 ASP Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 70 ARG Chi-restraints excluded: chain Ae residue 86 ASP Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ad residue 6 GLN Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 31 GLU Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 93 ASP Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 125 ASP Chi-restraints excluded: chain AS residue 13 LEU Chi-restraints excluded: chain AS residue 20 ILE Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 28 ILE Chi-restraints excluded: chain AS residue 35 VAL Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 124 GLU Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 152 ASN Chi-restraints excluded: chain AS residue 157 GLU Chi-restraints excluded: chain AS residue 165 THR Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 85 ASN Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 156 CYS Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 329 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 257 ASN ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN AV 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27255 Z= 0.227 Angle : 0.684 21.392 37145 Z= 0.339 Chirality : 0.046 0.255 4191 Planarity : 0.006 0.186 4931 Dihedral : 5.900 73.748 3757 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.47 % Favored : 88.27 % Rotamer: Outliers : 5.96 % Allowed : 25.45 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.20 (0.14), residues: 3435 helix: 0.91 (0.24), residues: 523 sheet: -0.68 (0.16), residues: 1034 loop : -2.76 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP r 331 HIS 0.003 0.001 HIS 3 218 PHE 0.026 0.001 PHE p 250 TYR 0.019 0.001 TYR F 222 ARG 0.009 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 482 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 19 CYS cc_start: 0.5045 (OUTLIER) cc_final: 0.4587 (p) REVERT: 3 30 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.7891 (ttt90) REVERT: 3 162 PRO cc_start: 0.7904 (Cg_exo) cc_final: 0.7560 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7934 (mmp-170) cc_final: 0.7492 (mpp80) REVERT: D 1 MET cc_start: 0.7448 (tmm) cc_final: 0.6999 (tmm) REVERT: D 33 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7522 (mm-30) REVERT: D 38 MET cc_start: 0.7431 (ptp) cc_final: 0.6822 (ptp) REVERT: D 48 LEU cc_start: 0.8809 (mp) cc_final: 0.8597 (mp) REVERT: D 60 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6724 (tm-30) REVERT: D 90 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6577 (t70) REVERT: D 138 TRP cc_start: 0.8094 (m100) cc_final: 0.7781 (m100) REVERT: E 14 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6212 (tmmt) REVERT: E 38 MET cc_start: 0.8659 (mtp) cc_final: 0.8386 (mtp) REVERT: F 1 MET cc_start: 0.7829 (ttt) cc_final: 0.7213 (ttt) REVERT: F 73 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7468 (p0) REVERT: G 17 ASP cc_start: 0.8540 (t0) cc_final: 0.8340 (t0) REVERT: G 38 MET cc_start: 0.7965 (mtt) cc_final: 0.7765 (mtt) REVERT: G 142 ASN cc_start: 0.9080 (t0) cc_final: 0.8825 (t0) REVERT: G 148 TYR cc_start: 0.7036 (t80) cc_final: 0.6748 (t80) REVERT: G 159 LEU cc_start: 0.6637 (mm) cc_final: 0.6214 (mt) REVERT: G 206 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7911 (tm-30) REVERT: p 58 PHE cc_start: 0.3408 (p90) cc_final: 0.2736 (p90) REVERT: p 403 GLN cc_start: 0.8651 (mm-40) cc_final: 0.7733 (mm-40) REVERT: q 16 ASP cc_start: 0.8960 (t0) cc_final: 0.8628 (t0) REVERT: q 43 ASP cc_start: 0.7938 (m-30) cc_final: 0.7276 (m-30) REVERT: q 454 ASP cc_start: 0.8705 (m-30) cc_final: 0.8401 (m-30) REVERT: r 82 TYR cc_start: 0.7391 (m-80) cc_final: 0.7002 (m-80) REVERT: r 207 ASN cc_start: 0.8208 (p0) cc_final: 0.7653 (p0) REVERT: r 258 LYS cc_start: 0.6078 (tttp) cc_final: 0.4382 (ptmt) REVERT: r 331 TRP cc_start: 0.5734 (OUTLIER) cc_final: 0.5498 (p90) REVERT: r 375 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6380 (tttt) REVERT: s 29 LEU cc_start: 0.8482 (tp) cc_final: 0.8163 (tp) REVERT: s 66 GLU cc_start: 0.8421 (tp30) cc_final: 0.8152 (tp30) REVERT: s 364 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7334 (p90) REVERT: s 379 ASN cc_start: 0.7852 (t0) cc_final: 0.7344 (t0) REVERT: s 414 ASN cc_start: 0.8374 (m-40) cc_final: 0.8099 (t0) REVERT: s 458 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8764 (mt) REVERT: s 461 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8231 (p90) REVERT: AV 54 TYR cc_start: 0.8719 (m-80) cc_final: 0.8281 (m-80) REVERT: Aa 126 GLU cc_start: 0.7656 (tt0) cc_final: 0.7433 (tt0) REVERT: Ae 18 ASP cc_start: 0.8387 (t0) cc_final: 0.7964 (t70) REVERT: Ae 97 MET cc_start: 0.8521 (mmt) cc_final: 0.8013 (mmt) REVERT: Ae 101 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7981 (mm-30) REVERT: Ad 52 ASN cc_start: 0.9150 (t0) cc_final: 0.8787 (t0) REVERT: AS 112 ASP cc_start: 0.8552 (m-30) cc_final: 0.8115 (m-30) REVERT: AT 104 TYR cc_start: 0.8761 (t80) cc_final: 0.5976 (m-10) REVERT: AT 144 TYR cc_start: 0.8869 (m-80) cc_final: 0.8431 (m-80) outliers start: 176 outliers final: 139 residues processed: 610 average time/residue: 0.3744 time to fit residues: 359.9209 Evaluate side-chains 609 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 461 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 108 ASN Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 264 VAL Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 410 VAL Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 476 LEU Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain q residue 452 ASN Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 37 ASP Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 208 ASP Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 309 ASN Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 338 GLN Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 22 PHE Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 226 ASP Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 345 VAL Chi-restraints excluded: chain s residue 364 TYR Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain s residue 461 PHE Chi-restraints excluded: chain s residue 477 ASN Chi-restraints excluded: chain AV residue 40 TYR Chi-restraints excluded: chain AV residue 93 ASP Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 86 ASP Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 70 ARG Chi-restraints excluded: chain Ae residue 86 ASP Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 93 ASP Chi-restraints excluded: chain Ad residue 110 SER Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 125 ASP Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 28 ILE Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 124 GLU Chi-restraints excluded: chain AS residue 136 ILE Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 157 GLU Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 18 LYS Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 196 optimal weight: 0.4980 chunk 99 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 chunk 224 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 259 optimal weight: 1.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 6 GLN ** AV 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 88 GLN Ae 22 GLN ** Ae 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27255 Z= 0.345 Angle : 0.719 20.953 37145 Z= 0.358 Chirality : 0.048 0.236 4191 Planarity : 0.006 0.184 4931 Dihedral : 5.900 69.312 3756 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.26 % Favored : 87.48 % Rotamer: Outliers : 6.06 % Allowed : 25.92 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.23 (0.14), residues: 3435 helix: 0.84 (0.23), residues: 525 sheet: -0.68 (0.16), residues: 1034 loop : -2.79 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP r 331 HIS 0.005 0.001 HIS F 182 PHE 0.018 0.002 PHE s 58 TYR 0.023 0.002 TYR p 480 ARG 0.009 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 453 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 19 CYS cc_start: 0.4902 (OUTLIER) cc_final: 0.4507 (p) REVERT: 3 30 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.7798 (ttt90) REVERT: 3 162 PRO cc_start: 0.8028 (Cg_exo) cc_final: 0.7731 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7945 (mmp-170) cc_final: 0.7497 (mpp80) REVERT: 3 212 ASP cc_start: 0.8127 (m-30) cc_final: 0.7916 (m-30) REVERT: D 33 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7662 (mm-30) REVERT: D 38 MET cc_start: 0.7506 (ptp) cc_final: 0.7256 (ptp) REVERT: D 60 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6737 (tm-30) REVERT: D 90 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6638 (t70) REVERT: D 138 TRP cc_start: 0.8132 (m100) cc_final: 0.7778 (m100) REVERT: D 201 ARG cc_start: 0.8536 (ttm110) cc_final: 0.8116 (mtp-110) REVERT: E 14 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6262 (tmmt) REVERT: E 38 MET cc_start: 0.8737 (mtp) cc_final: 0.8354 (mtp) REVERT: E 79 LYS cc_start: 0.8003 (mmmt) cc_final: 0.7716 (mmtm) REVERT: F 1 MET cc_start: 0.7825 (ttt) cc_final: 0.7391 (ttt) REVERT: F 73 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7464 (p0) REVERT: F 217 VAL cc_start: 0.9018 (t) cc_final: 0.8561 (p) REVERT: G 38 MET cc_start: 0.8049 (mtt) cc_final: 0.7682 (mtm) REVERT: G 148 TYR cc_start: 0.7022 (t80) cc_final: 0.6810 (t80) REVERT: G 159 LEU cc_start: 0.6634 (mm) cc_final: 0.6147 (mt) REVERT: p 58 PHE cc_start: 0.3576 (p90) cc_final: 0.2918 (p90) REVERT: p 403 GLN cc_start: 0.8711 (mm-40) cc_final: 0.7735 (mm-40) REVERT: q 16 ASP cc_start: 0.8966 (t0) cc_final: 0.8627 (t0) REVERT: q 450 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7824 (t0) REVERT: q 454 ASP cc_start: 0.8730 (m-30) cc_final: 0.8456 (m-30) REVERT: r 82 TYR cc_start: 0.7433 (m-80) cc_final: 0.6997 (m-80) REVERT: r 207 ASN cc_start: 0.8258 (p0) cc_final: 0.7681 (p0) REVERT: r 258 LYS cc_start: 0.6255 (tttp) cc_final: 0.4378 (ptmt) REVERT: r 331 TRP cc_start: 0.5817 (OUTLIER) cc_final: 0.5600 (p90) REVERT: r 375 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6326 (tttt) REVERT: r 377 ARG cc_start: 0.7836 (mpp-170) cc_final: 0.7599 (mtp-110) REVERT: r 462 GLU cc_start: 0.7850 (tt0) cc_final: 0.7287 (tm-30) REVERT: s 29 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8157 (tp) REVERT: s 66 GLU cc_start: 0.8303 (tp30) cc_final: 0.8097 (tp30) REVERT: s 364 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7384 (p90) REVERT: s 375 LYS cc_start: 0.7007 (tmtt) cc_final: 0.6035 (pptt) REVERT: s 379 ASN cc_start: 0.7857 (t0) cc_final: 0.7354 (t0) REVERT: s 414 ASN cc_start: 0.8402 (m-40) cc_final: 0.8119 (t0) REVERT: s 461 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8256 (p90) REVERT: AV 54 TYR cc_start: 0.8774 (m-80) cc_final: 0.8354 (m-80) REVERT: Ae 18 ASP cc_start: 0.8416 (t0) cc_final: 0.7985 (t70) REVERT: Ae 97 MET cc_start: 0.8600 (mmt) cc_final: 0.7616 (mmt) REVERT: Ae 101 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7994 (mm-30) REVERT: Ae 126 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7276 (mt-10) REVERT: Ad 52 ASN cc_start: 0.9096 (t0) cc_final: 0.8728 (t0) REVERT: AT 104 TYR cc_start: 0.8820 (t80) cc_final: 0.5957 (m-10) REVERT: AT 144 TYR cc_start: 0.8863 (m-80) cc_final: 0.8502 (m-80) outliers start: 179 outliers final: 155 residues processed: 587 average time/residue: 0.3811 time to fit residues: 356.4496 Evaluate side-chains 603 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 438 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 108 ASN Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 149 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 249 CYS Chi-restraints excluded: chain p residue 264 VAL Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 320 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 339 LEU Chi-restraints excluded: chain p residue 367 VAL Chi-restraints excluded: chain p residue 410 VAL Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 424 THR Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 417 ILE Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 450 ASN Chi-restraints excluded: chain r residue 28 ILE Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 37 ASP Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 208 ASP Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 297 LEU Chi-restraints excluded: chain r residue 309 ASN Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 338 GLN Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 447 GLU Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 29 LEU Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 226 ASP Chi-restraints excluded: chain s residue 260 THR Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 345 VAL Chi-restraints excluded: chain s residue 364 TYR Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain s residue 461 PHE Chi-restraints excluded: chain s residue 477 ASN Chi-restraints excluded: chain AV residue 24 VAL Chi-restraints excluded: chain AV residue 93 ASP Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 3 CYS Chi-restraints excluded: chain Aa residue 43 CYS Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 84 GLN Chi-restraints excluded: chain Aa residue 86 ASP Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Ae residue 14 ILE Chi-restraints excluded: chain Ae residue 70 ARG Chi-restraints excluded: chain Ae residue 72 LEU Chi-restraints excluded: chain Ae residue 86 ASP Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 50 LEU Chi-restraints excluded: chain Ad residue 51 THR Chi-restraints excluded: chain Ad residue 58 SER Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 93 ASP Chi-restraints excluded: chain Ad residue 110 SER Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 125 ASP Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 28 ILE Chi-restraints excluded: chain AS residue 35 VAL Chi-restraints excluded: chain AS residue 48 THR Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 124 GLU Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 152 ASN Chi-restraints excluded: chain AS residue 157 GLU Chi-restraints excluded: chain AS residue 165 THR Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 85 ASN Chi-restraints excluded: chain AT residue 122 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 0.7980 chunk 315 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 277 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 306 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 365 ASN ** q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN r 233 ASN ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 379 ASN AV 6 GLN Ae 22 GLN ** Ae 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27255 Z= 0.190 Angle : 0.677 12.505 37145 Z= 0.334 Chirality : 0.046 0.242 4191 Planarity : 0.005 0.098 4931 Dihedral : 5.702 67.845 3756 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.57 % Favored : 89.23 % Rotamer: Outliers : 5.21 % Allowed : 26.80 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.02 (0.14), residues: 3435 helix: 1.13 (0.24), residues: 517 sheet: -0.53 (0.16), residues: 1029 loop : -2.67 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP r 331 HIS 0.003 0.001 HIS 3 218 PHE 0.016 0.001 PHE D 137 TYR 0.021 0.001 TYR p 480 ARG 0.007 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 517 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 19 CYS cc_start: 0.4876 (OUTLIER) cc_final: 0.4432 (p) REVERT: 3 30 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.7896 (ttt90) REVERT: 3 148 TYR cc_start: 0.8010 (t80) cc_final: 0.7672 (t80) REVERT: 3 162 PRO cc_start: 0.7845 (Cg_exo) cc_final: 0.7508 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7926 (mmp-170) cc_final: 0.7483 (mpp80) REVERT: D 33 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7570 (mm-30) REVERT: D 60 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6767 (tm-30) REVERT: D 87 THR cc_start: 0.7399 (t) cc_final: 0.6704 (m) REVERT: D 90 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6480 (t70) REVERT: D 136 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7176 (mtt90) REVERT: D 138 TRP cc_start: 0.8051 (m100) cc_final: 0.7732 (m100) REVERT: D 201 ARG cc_start: 0.8536 (ttm110) cc_final: 0.8098 (mtp-110) REVERT: E 14 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6311 (tmmt) REVERT: E 38 MET cc_start: 0.8732 (mtp) cc_final: 0.8355 (mtp) REVERT: E 157 SER cc_start: 0.8396 (m) cc_final: 0.8100 (p) REVERT: F 1 MET cc_start: 0.7622 (ttt) cc_final: 0.7200 (ttt) REVERT: G 38 MET cc_start: 0.8011 (mtt) cc_final: 0.7684 (mtm) REVERT: G 142 ASN cc_start: 0.9097 (t0) cc_final: 0.8846 (t0) REVERT: G 148 TYR cc_start: 0.7009 (t80) cc_final: 0.6750 (t80) REVERT: G 159 LEU cc_start: 0.6748 (mm) cc_final: 0.6289 (mt) REVERT: p 58 PHE cc_start: 0.3592 (p90) cc_final: 0.2908 (p90) REVERT: p 243 ASP cc_start: 0.8295 (t0) cc_final: 0.7615 (m-30) REVERT: q 16 ASP cc_start: 0.8939 (t0) cc_final: 0.8625 (t0) REVERT: q 43 ASP cc_start: 0.7966 (m-30) cc_final: 0.7239 (m-30) REVERT: q 454 ASP cc_start: 0.8689 (m-30) cc_final: 0.8325 (m-30) REVERT: r 82 TYR cc_start: 0.7432 (m-80) cc_final: 0.7028 (m-80) REVERT: r 207 ASN cc_start: 0.8312 (p0) cc_final: 0.7750 (p0) REVERT: r 258 LYS cc_start: 0.6160 (tttp) cc_final: 0.4301 (ptmt) REVERT: r 331 TRP cc_start: 0.5853 (OUTLIER) cc_final: 0.5643 (p90) REVERT: r 375 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6174 (tttt) REVERT: s 27 LYS cc_start: 0.7711 (tppt) cc_final: 0.7192 (mmmt) REVERT: s 29 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8215 (tp) REVERT: s 66 GLU cc_start: 0.8389 (tp30) cc_final: 0.8152 (tp30) REVERT: s 364 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7220 (p90) REVERT: s 375 LYS cc_start: 0.6938 (tmtt) cc_final: 0.5867 (pptt) REVERT: s 379 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7198 (t0) REVERT: s 414 ASN cc_start: 0.8342 (m-40) cc_final: 0.8044 (t0) REVERT: s 461 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8133 (p90) REVERT: AV 54 TYR cc_start: 0.8682 (m-80) cc_final: 0.8206 (m-80) REVERT: AV 127 LEU cc_start: 0.8340 (tt) cc_final: 0.8073 (tt) REVERT: Aa 126 GLU cc_start: 0.7467 (tt0) cc_final: 0.7219 (tt0) REVERT: Ae 18 ASP cc_start: 0.8414 (t0) cc_final: 0.8098 (t70) REVERT: Ae 97 MET cc_start: 0.8526 (mmt) cc_final: 0.8053 (mmt) REVERT: Ae 101 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8101 (mm-30) REVERT: Ad 52 ASN cc_start: 0.9176 (t0) cc_final: 0.8832 (t0) REVERT: AS 112 ASP cc_start: 0.8496 (m-30) cc_final: 0.8068 (m-30) REVERT: AS 137 SER cc_start: 0.9051 (t) cc_final: 0.8604 (p) REVERT: AT 104 TYR cc_start: 0.8723 (t80) cc_final: 0.5977 (m-10) REVERT: AT 135 ASP cc_start: 0.8494 (m-30) cc_final: 0.8108 (m-30) REVERT: AT 144 TYR cc_start: 0.8893 (m-80) cc_final: 0.8477 (m-80) outliers start: 154 outliers final: 121 residues processed: 628 average time/residue: 0.3734 time to fit residues: 370.0479 Evaluate side-chains 629 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 499 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 108 ASN Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 19 CYS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 339 LEU Chi-restraints excluded: chain p residue 410 VAL Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain q residue 452 ASN Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 37 ASP Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 29 LEU Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 285 VAL Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 364 TYR Chi-restraints excluded: chain s residue 379 ASN Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain s residue 461 PHE Chi-restraints excluded: chain s residue 477 ASN Chi-restraints excluded: chain AV residue 24 VAL Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 86 ASP Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Ae residue 70 ARG Chi-restraints excluded: chain Ae residue 72 LEU Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 93 ASP Chi-restraints excluded: chain Ad residue 110 SER Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 28 ILE Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 124 GLU Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 152 ASN Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 137 SER Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Chi-restraints excluded: chain AT residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 340 optimal weight: 8.9990 chunk 313 optimal weight: 0.0370 chunk 271 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 209 optimal weight: 0.0970 chunk 166 optimal weight: 9.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 379 ASN AV 6 GLN ** AV 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27255 Z= 0.197 Angle : 0.680 11.384 37145 Z= 0.336 Chirality : 0.046 0.239 4191 Planarity : 0.005 0.112 4931 Dihedral : 5.461 64.256 3753 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.00 % Favored : 88.85 % Rotamer: Outliers : 4.84 % Allowed : 27.45 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -1.95 (0.14), residues: 3435 helix: 1.21 (0.24), residues: 512 sheet: -0.50 (0.16), residues: 1037 loop : -2.62 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP r 331 HIS 0.002 0.001 HIS 3 218 PHE 0.018 0.001 PHE D 92 TYR 0.021 0.001 TYR p 480 ARG 0.010 0.000 ARG r 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6870 Ramachandran restraints generated. 3435 Oldfield, 0 Emsley, 3435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 505 time to evaluate : 3.164 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: 3 19 CYS cc_start: 0.4562 (OUTLIER) cc_final: 0.3588 (p) REVERT: 3 30 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.7762 (ttt90) REVERT: 3 155 THR cc_start: 0.6566 (t) cc_final: 0.6297 (t) REVERT: 3 162 PRO cc_start: 0.7758 (Cg_exo) cc_final: 0.7414 (Cg_endo) REVERT: 3 180 ARG cc_start: 0.7924 (mmp-170) cc_final: 0.7473 (mpp80) REVERT: D 33 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7542 (mm-30) REVERT: D 60 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6756 (tm-30) REVERT: D 87 THR cc_start: 0.7421 (t) cc_final: 0.6709 (m) REVERT: D 90 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6505 (t70) REVERT: D 136 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7187 (mtt90) REVERT: D 138 TRP cc_start: 0.8051 (m100) cc_final: 0.7787 (m100) REVERT: D 201 ARG cc_start: 0.8476 (ttm110) cc_final: 0.8063 (mtp-110) REVERT: E 14 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6382 (tmmt) REVERT: E 38 MET cc_start: 0.8727 (mtp) cc_final: 0.8349 (mtp) REVERT: E 157 SER cc_start: 0.8500 (m) cc_final: 0.8259 (p) REVERT: F 1 MET cc_start: 0.7644 (ttt) cc_final: 0.7276 (ttt) REVERT: G 142 ASN cc_start: 0.9116 (t0) cc_final: 0.8894 (t0) REVERT: G 148 TYR cc_start: 0.6985 (t80) cc_final: 0.6776 (t80) REVERT: G 159 LEU cc_start: 0.6684 (mm) cc_final: 0.6232 (mt) REVERT: p 58 PHE cc_start: 0.3590 (p90) cc_final: 0.2903 (p90) REVERT: p 76 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8315 (ttpp) REVERT: p 243 ASP cc_start: 0.8270 (t0) cc_final: 0.7641 (m-30) REVERT: p 439 ASP cc_start: 0.8955 (m-30) cc_final: 0.8731 (t0) REVERT: q 16 ASP cc_start: 0.8877 (t0) cc_final: 0.8619 (t0) REVERT: q 43 ASP cc_start: 0.7986 (m-30) cc_final: 0.7241 (m-30) REVERT: r 82 TYR cc_start: 0.7444 (m-80) cc_final: 0.7030 (m-80) REVERT: r 207 ASN cc_start: 0.8301 (p0) cc_final: 0.7572 (p0) REVERT: r 258 LYS cc_start: 0.6207 (tttp) cc_final: 0.4321 (ptmt) REVERT: r 331 TRP cc_start: 0.5973 (OUTLIER) cc_final: 0.5464 (p90) REVERT: r 375 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6184 (tttt) REVERT: r 462 GLU cc_start: 0.7841 (tt0) cc_final: 0.7338 (tm-30) REVERT: r 467 CYS cc_start: 0.3534 (OUTLIER) cc_final: 0.2840 (m) REVERT: s 27 LYS cc_start: 0.7642 (tppt) cc_final: 0.7082 (mmmt) REVERT: s 58 PHE cc_start: 0.5201 (m-80) cc_final: 0.4794 (m-80) REVERT: s 66 GLU cc_start: 0.8412 (tp30) cc_final: 0.8193 (tp30) REVERT: s 364 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7968 (p90) REVERT: s 375 LYS cc_start: 0.6786 (tmtt) cc_final: 0.5835 (pptt) REVERT: s 379 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7231 (t0) REVERT: s 414 ASN cc_start: 0.8318 (m-40) cc_final: 0.8001 (t0) REVERT: s 458 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8737 (mt) REVERT: s 461 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8150 (p90) REVERT: AV 54 TYR cc_start: 0.8701 (m-80) cc_final: 0.8247 (m-80) REVERT: Aa 126 GLU cc_start: 0.7403 (tt0) cc_final: 0.7171 (tt0) REVERT: Ae 18 ASP cc_start: 0.8540 (t0) cc_final: 0.8113 (t70) REVERT: Ae 97 MET cc_start: 0.8532 (mmt) cc_final: 0.8113 (mmt) REVERT: Ae 101 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8147 (mm-30) REVERT: Ad 18 ASP cc_start: 0.8737 (t0) cc_final: 0.8361 (t0) REVERT: Ad 52 ASN cc_start: 0.9154 (t0) cc_final: 0.8815 (t0) REVERT: AS 112 ASP cc_start: 0.8481 (m-30) cc_final: 0.8079 (m-30) REVERT: AS 137 SER cc_start: 0.9061 (t) cc_final: 0.8618 (p) REVERT: AT 104 TYR cc_start: 0.8721 (t80) cc_final: 0.5988 (m-10) REVERT: AT 135 ASP cc_start: 0.8509 (m-30) cc_final: 0.8206 (m-30) REVERT: AT 144 TYR cc_start: 0.8911 (m-80) cc_final: 0.8515 (m-80) outliers start: 143 outliers final: 122 residues processed: 607 average time/residue: 0.3774 time to fit residues: 361.6820 Evaluate side-chains 624 residues out of total 2955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 492 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 19 CYS Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 108 ASN Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 211 THR Chi-restraints excluded: chain p residue 212 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 242 TRP Chi-restraints excluded: chain p residue 264 VAL Chi-restraints excluded: chain p residue 274 LEU Chi-restraints excluded: chain p residue 300 CYS Chi-restraints excluded: chain p residue 332 THR Chi-restraints excluded: chain p residue 339 LEU Chi-restraints excluded: chain p residue 410 VAL Chi-restraints excluded: chain p residue 419 THR Chi-restraints excluded: chain p residue 484 VAL Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain q residue 213 VAL Chi-restraints excluded: chain q residue 265 LEU Chi-restraints excluded: chain q residue 288 TYR Chi-restraints excluded: chain q residue 315 PHE Chi-restraints excluded: chain q residue 335 GLU Chi-restraints excluded: chain q residue 337 THR Chi-restraints excluded: chain q residue 345 VAL Chi-restraints excluded: chain q residue 443 THR Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 37 ASP Chi-restraints excluded: chain r residue 81 VAL Chi-restraints excluded: chain r residue 208 ASP Chi-restraints excluded: chain r residue 212 VAL Chi-restraints excluded: chain r residue 213 VAL Chi-restraints excluded: chain r residue 222 VAL Chi-restraints excluded: chain r residue 331 TRP Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 344 PHE Chi-restraints excluded: chain r residue 368 THR Chi-restraints excluded: chain r residue 375 LYS Chi-restraints excluded: chain r residue 390 LEU Chi-restraints excluded: chain r residue 410 VAL Chi-restraints excluded: chain r residue 448 PHE Chi-restraints excluded: chain r residue 467 CYS Chi-restraints excluded: chain r residue 477 ASN Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 28 ILE Chi-restraints excluded: chain s residue 202 VAL Chi-restraints excluded: chain s residue 274 LEU Chi-restraints excluded: chain s residue 285 VAL Chi-restraints excluded: chain s residue 288 TYR Chi-restraints excluded: chain s residue 308 LEU Chi-restraints excluded: chain s residue 315 PHE Chi-restraints excluded: chain s residue 332 THR Chi-restraints excluded: chain s residue 339 LEU Chi-restraints excluded: chain s residue 364 TYR Chi-restraints excluded: chain s residue 367 VAL Chi-restraints excluded: chain s residue 379 ASN Chi-restraints excluded: chain s residue 412 THR Chi-restraints excluded: chain s residue 441 VAL Chi-restraints excluded: chain s residue 458 LEU Chi-restraints excluded: chain s residue 461 PHE Chi-restraints excluded: chain s residue 477 ASN Chi-restraints excluded: chain AV residue 4 ASN Chi-restraints excluded: chain AV residue 24 VAL Chi-restraints excluded: chain AV residue 93 ASP Chi-restraints excluded: chain AV residue 96 VAL Chi-restraints excluded: chain AV residue 98 THR Chi-restraints excluded: chain AV residue 120 VAL Chi-restraints excluded: chain Aa residue 43 CYS Chi-restraints excluded: chain Aa residue 96 VAL Chi-restraints excluded: chain Aa residue 101 GLU Chi-restraints excluded: chain Aa residue 122 SER Chi-restraints excluded: chain Ae residue 17 THR Chi-restraints excluded: chain Ae residue 70 ARG Chi-restraints excluded: chain Ae residue 72 LEU Chi-restraints excluded: chain Ae residue 110 SER Chi-restraints excluded: chain Ad residue 17 THR Chi-restraints excluded: chain Ad residue 43 CYS Chi-restraints excluded: chain Ad residue 70 ARG Chi-restraints excluded: chain Ad residue 93 ASP Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain AS residue 21 VAL Chi-restraints excluded: chain AS residue 25 PHE Chi-restraints excluded: chain AS residue 53 VAL Chi-restraints excluded: chain AS residue 81 ILE Chi-restraints excluded: chain AS residue 124 GLU Chi-restraints excluded: chain AS residue 136 ILE Chi-restraints excluded: chain AS residue 142 VAL Chi-restraints excluded: chain AS residue 152 ASN Chi-restraints excluded: chain AS residue 171 PHE Chi-restraints excluded: chain AT residue 25 PHE Chi-restraints excluded: chain AT residue 38 VAL Chi-restraints excluded: chain AT residue 43 SER Chi-restraints excluded: chain AT residue 128 THR Chi-restraints excluded: chain AT residue 152 ASN Chi-restraints excluded: chain AT residue 163 ASP Chi-restraints excluded: chain AT residue 165 THR Chi-restraints excluded: chain AT residue 173 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 6.9990 chunk 289 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 250 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 75 optimal weight: 9.9990 chunk 271 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 ASN G 161 GLN ** q 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 214 ASN ** r 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 379 ASN AV 6 GLN ** AV 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 4 ASN ** AT 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.127448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099591 restraints weight = 62127.464| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.37 r_work: 0.3288 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27255 Z= 0.176 Angle : 0.671 10.627 37145 Z= 0.331 Chirality : 0.046 0.241 4191 Planarity : 0.005 0.104 4931 Dihedral : 5.262 61.336 3751 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.25 % Favored : 89.55 % Rotamer: Outliers : 4.33 % Allowed : 28.02 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3435 helix: 1.20 (0.24), residues: 520 sheet: -0.33 (0.16), residues: 1013 loop : -2.55 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP r 331 HIS 0.002 0.000 HIS 3 218 PHE 0.015 0.001 PHE D 137 TYR 0.019 0.001 TYR p 480 ARG 0.009 0.000 ARGAV 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7224.30 seconds wall clock time: 130 minutes 51.69 seconds (7851.69 seconds total)