Starting phenix.real_space_refine on Thu Feb 15 11:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a0e_15052/02_2024/8a0e_15052_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a0e_15052/02_2024/8a0e_15052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a0e_15052/02_2024/8a0e_15052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a0e_15052/02_2024/8a0e_15052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a0e_15052/02_2024/8a0e_15052_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a0e_15052/02_2024/8a0e_15052_updated.pdb" } resolution = 2.8 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= 0.002 sd= 0.049 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 70 5.16 5 C 7638 2.51 5 N 2069 2.21 5 O 2297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12082 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2770 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 356, 2767 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 16, 'TRANS': 339} Conformer: "B" Number of residues, atoms: 356, 2767 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 16, 'TRANS': 339} bond proxies already assigned to first conformer: 2820 Chain: "B" Number of atoms: 2736 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 352, 2733 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 Conformer: "C" Number of residues, atoms: 352, 2733 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 bond proxies already assigned to first conformer: 2785 Chain: "C" Number of atoms: 2724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 350, 2720 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSS:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 350, 2720 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSS:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2771 Chain: "D" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2597 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSS:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1049 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N ALA A 11 " occ=0.83 ... (3 atoms not shown) pdb=" CB ALA A 11 " occ=0.83 residue: pdb=" N LEU A 14 " occ=0.88 ... (6 atoms not shown) pdb=" CD2 LEU A 14 " occ=0.88 residue: pdb=" N ALA A 15 " occ=0.94 ... (3 atoms not shown) pdb=" CB ALA A 15 " occ=0.94 residue: pdb=" N HIS A 20 " occ=0.95 ... (8 atoms not shown) pdb=" NE2 HIS A 20 " occ=0.95 residue: pdb=" N PRO A 26 " occ=0.91 ... (5 atoms not shown) pdb=" CD PRO A 26 " occ=0.91 residue: pdb=" N ALA B 11 " occ=0.82 ... (3 atoms not shown) pdb=" CB ALA B 11 " occ=0.82 residue: pdb=" N LEU B 14 " occ=0.82 ... (6 atoms not shown) pdb=" CD2 LEU B 14 " occ=0.82 residue: pdb=" N ALA B 15 " occ=0.90 ... (3 atoms not shown) pdb=" CB ALA B 15 " occ=0.90 residue: pdb=" N HIS B 20 " occ=0.91 ... (8 atoms not shown) pdb=" NE2 HIS B 20 " occ=0.91 residue: pdb=" N ALA C 11 " occ=0.83 ... (3 atoms not shown) pdb=" CB ALA C 11 " occ=0.83 residue: pdb=" N LEU C 14 " occ=0.88 ... (6 atoms not shown) pdb=" CD2 LEU C 14 " occ=0.88 residue: pdb=" N ALA C 15 " occ=0.94 ... (3 atoms not shown) pdb=" CB ALA C 15 " occ=0.94 ... (remaining 6 not shown) Time building chain proxies: 10.24, per 1000 atoms: 0.85 Number of scatterers: 12082 At special positions: 0 Unit cell: (92.02, 96.32, 149.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 8 15.00 O 2297 8.00 N 2069 7.00 C 7638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 73 " distance=2.04 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: 4.49 Conformation dependent library (CDL) restraints added in 3.6 seconds 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 11 sheets defined 44.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 11 through 17 removed outlier: 3.693A pdb=" N ALA A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.891A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 73 removed outlier: 4.196A pdb=" N ASN A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 4.441A pdb=" N ARG A 117 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 118 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN A 121 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 removed outlier: 3.827A pdb=" N ASP A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 173 through 196 removed outlier: 3.875A pdb=" N LYS A 178 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 179 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 180 " --> pdb=" O CYS A 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 181 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N MET A 184 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.844A pdb=" N THR A 196 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.773A pdb=" N LYS A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 Processing helix chain 'A' and resid 240 through 250 removed outlier: 4.048A pdb=" N TYR A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.540A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 297 removed outlier: 3.970A pdb=" N MET A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.699A pdb=" N VAL A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 326' Processing helix chain 'A' and resid 343 through 353 Proline residue: A 348 - end of helix removed outlier: 3.605A pdb=" N GLU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'B' and resid 11 through 17 Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.543A pdb=" N GLU B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLY B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 73 removed outlier: 4.046A pdb=" N ASN B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.733A pdb=" N ILE B 116 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG B 117 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 121 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 removed outlier: 4.064A pdb=" N ASP B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 173 through 195 removed outlier: 3.826A pdb=" N LYS B 178 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B 179 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 180 " --> pdb=" O CYS B 177 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET B 184 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.749A pdb=" N VAL B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET B 192 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 193 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 240 through 250 removed outlier: 4.230A pdb=" N TYR B 250 " --> pdb=" O PHE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.818A pdb=" N ALA B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.960A pdb=" N MET B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.916A pdb=" N VAL B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 326' Processing helix chain 'B' and resid 343 through 354 Proline residue: B 348 - end of helix removed outlier: 3.551A pdb=" N GLU B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'C' and resid 11 through 17 Processing helix chain 'C' and resid 36 through 38 No H-bonds generated for 'chain 'C' and resid 36 through 38' Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.510A pdb=" N GLU C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 Processing helix chain 'C' and resid 85 through 88 No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 111 through 121 removed outlier: 3.840A pdb=" N ILE C 116 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 117 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 121 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 removed outlier: 4.096A pdb=" N ASP C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 173 through 196 removed outlier: 3.503A pdb=" N LYS C 178 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE C 179 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU C 180 " --> pdb=" O CSS C 177 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP C 181 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET C 184 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 3.653A pdb=" N ASP C 188 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 193 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 196 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 214 Processing helix chain 'C' and resid 220 through 226 Processing helix chain 'C' and resid 240 through 250 removed outlier: 3.951A pdb=" N TYR C 250 " --> pdb=" O PHE C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 271 Processing helix chain 'C' and resid 285 through 297 removed outlier: 3.993A pdb=" N MET C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.805A pdb=" N VAL C 325 " --> pdb=" O PRO C 321 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 326' Processing helix chain 'C' and resid 343 through 353 Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 42 through 51 removed outlier: 3.838A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 73 removed outlier: 4.019A pdb=" N ASN D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 88 No H-bonds generated for 'chain 'D' and resid 85 through 88' Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.552A pdb=" N ILE D 116 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG D 117 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 121 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 142 removed outlier: 3.616A pdb=" N GLU D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 173 through 196 removed outlier: 3.661A pdb=" N LYS D 178 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE D 179 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU D 180 " --> pdb=" O CSS D 177 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 181 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET D 184 " --> pdb=" O ASP D 181 " (cutoff:3.500A) Proline residue: D 185 - end of helix removed outlier: 3.967A pdb=" N THR D 196 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 Processing helix chain 'D' and resid 220 through 226 Processing helix chain 'D' and resid 240 through 250 removed outlier: 4.021A pdb=" N TYR D 250 " --> pdb=" O PHE D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.696A pdb=" N ARG D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 266 " --> pdb=" O ASP D 262 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 270 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 297 removed outlier: 3.839A pdb=" N MET D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 324 No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 343 through 354 Proline residue: D 348 - end of helix Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.563A pdb=" N GLU E 124 " --> pdb=" O LYS E 121 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN E 125 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 126 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 230 through 232 removed outlier: 6.751A pdb=" N TYR A 302 " --> pdb=" O MET A 278 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE A 280 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 304 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 337 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASN A 307 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL A 339 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 163 through 166 Processing sheet with id= C, first strand: chain 'B' and resid 230 through 232 removed outlier: 6.780A pdb=" N TYR B 302 " --> pdb=" O MET B 278 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE B 280 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 304 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 337 " --> pdb=" O TYR B 305 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 163 through 166 Processing sheet with id= E, first strand: chain 'C' and resid 230 through 232 removed outlier: 6.745A pdb=" N TYR C 302 " --> pdb=" O MET C 278 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ILE C 280 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 304 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 337 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN C 307 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL C 339 " --> pdb=" O ASN C 307 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 163 through 166 Processing sheet with id= G, first strand: chain 'D' and resid 230 through 232 removed outlier: 6.668A pdb=" N TYR D 302 " --> pdb=" O MET D 278 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE D 280 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 304 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL D 337 " --> pdb=" O TYR D 305 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 163 through 166 Processing sheet with id= I, first strand: chain 'E' and resid 17 through 21 Processing sheet with id= J, first strand: chain 'E' and resid 30 through 32 removed outlier: 6.811A pdb=" N VAL E 59 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET E 43 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS E 57 " --> pdb=" O MET E 43 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR E 45 " --> pdb=" O LYS E 55 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS E 55 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.572A pdb=" N ASN E 87 " --> pdb=" O VAL E 137 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 915 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: 2.87 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 4991 1.40 - 1.58: 7209 1.58 - 1.75: 16 1.75 - 1.93: 116 1.93 - 2.11: 2 Bond restraints: 12334 Sorted by residual: bond pdb=" CB CSS D 177 " pdb=" SG CSS D 177 " ideal model delta sigma weight residual 1.823 1.755 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CB CSS C 177 " pdb=" SG CSS C 177 " ideal model delta sigma weight residual 1.823 1.756 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O3 NAD D 402 " pdb=" PA NAD D 402 " ideal model delta sigma weight residual 1.653 1.603 0.050 2.00e-02 2.50e+03 6.31e+00 bond pdb=" O3 NAD A 401 " pdb=" PA NAD A 401 " ideal model delta sigma weight residual 1.653 1.603 0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" O3 NAD C 401 " pdb=" PA NAD C 401 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.11e+00 ... (remaining 12329 not shown) Histogram of bond angle deviations from ideal: 99.54 - 107.00: 415 107.00 - 114.46: 7203 114.46 - 121.93: 6519 121.93 - 129.39: 2526 129.39 - 136.85: 78 Bond angle restraints: 16741 Sorted by residual: angle pdb=" CA CYS A 177 " pdb=" C CYS A 177 " pdb=" O CYS A 177 " ideal model delta sigma weight residual 119.60 123.92 -4.32 1.17e+00 7.31e-01 1.36e+01 angle pdb=" PA NAD A 401 " pdb=" O3 NAD A 401 " pdb=" PN NAD A 401 " ideal model delta sigma weight residual 126.50 136.85 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N CYS A 177 " pdb=" CA CYS A 177 " pdb=" C CYS A 177 " ideal model delta sigma weight residual 112.90 108.56 4.34 1.31e+00 5.83e-01 1.10e+01 angle pdb=" PA NAD B 401 " pdb=" O3 NAD B 401 " pdb=" PN NAD B 401 " ideal model delta sigma weight residual 126.50 134.95 -8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" PA NAD C 401 " pdb=" O3 NAD C 401 " pdb=" PN NAD C 401 " ideal model delta sigma weight residual 126.50 134.07 -7.57 3.00e+00 1.11e-01 6.37e+00 ... (remaining 16736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 6922 18.16 - 36.31: 443 36.31 - 54.47: 90 54.47 - 72.63: 27 72.63 - 90.79: 32 Dihedral angle restraints: 7514 sinusoidal: 3119 harmonic: 4395 Sorted by residual: dihedral pdb=" CA CYS E 73 " pdb=" C CYS E 73 " pdb=" N PRO E 74 " pdb=" CA PRO E 74 " ideal model delta harmonic sigma weight residual 180.00 147.50 32.50 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 73 " pdb=" CB CYS E 73 " ideal model delta sinusoidal sigma weight residual -86.00 -136.15 50.15 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA GLY A 53 " pdb=" C GLY A 53 " pdb=" N PHE A 54 " pdb=" CA PHE A 54 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1447 0.047 - 0.095: 323 0.095 - 0.142: 105 0.142 - 0.190: 1 0.190 - 0.237: 5 Chirality restraints: 1881 Sorted by residual: chirality pdb=" C1D NAD C 401 " pdb=" C2D NAD C 401 " pdb=" N1N NAD C 401 " pdb=" O4D NAD C 401 " both_signs ideal model delta sigma weight residual False 2.41 2.65 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1D NAD A 401 " pdb=" C2D NAD A 401 " pdb=" N1N NAD A 401 " pdb=" O4D NAD A 401 " both_signs ideal model delta sigma weight residual False 2.41 2.65 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C1D NAD B 401 " pdb=" C2D NAD B 401 " pdb=" N1N NAD B 401 " pdb=" O4D NAD B 401 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1878 not shown) Planarity restraints: 2151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 402 " 0.034 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" C2N NAD D 402 " -0.052 2.00e-02 2.50e+03 pdb=" C3N NAD D 402 " -0.004 2.00e-02 2.50e+03 pdb=" C4N NAD D 402 " 0.012 2.00e-02 2.50e+03 pdb=" C5N NAD D 402 " -0.002 2.00e-02 2.50e+03 pdb=" C6N NAD D 402 " -0.004 2.00e-02 2.50e+03 pdb=" C7N NAD D 402 " 0.024 2.00e-02 2.50e+03 pdb=" N1N NAD D 402 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 36 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO E 37 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 37 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 37 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 202 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 203 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 203 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 203 " 0.023 5.00e-02 4.00e+02 ... (remaining 2148 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 376 2.72 - 3.27: 11499 3.27 - 3.81: 18031 3.81 - 4.36: 24780 4.36 - 4.90: 41368 Nonbonded interactions: 96054 Sorted by model distance: nonbonded pdb=" OG SER C 105 " pdb=" OG1 THR C 131 " model vdw 2.176 2.440 nonbonded pdb=" OG SER A 315 " pdb=" O1A NAD B 401 " model vdw 2.211 2.440 nonbonded pdb=" OG SER A 105 " pdb=" OG1 THR A 131 " model vdw 2.225 2.440 nonbonded pdb=" O GLU A 323 " pdb=" OG SER A 326 " model vdw 2.238 2.440 nonbonded pdb=" OG SER D 105 " pdb=" OG1 THR D 131 " model vdw 2.245 2.440 ... (remaining 96049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 79 or resid 84 through 104 or resid 106 through \ 176 or resid 178 through 239 or resid 241 through 285 or resid 287 through 363) \ ) selection = (chain 'B' and (resid 28 through 104 or resid 106 through 176 or resid 178 throu \ gh 239 or resid 241 through 285 or resid 287 through 363)) selection = (chain 'C' and (resid 28 through 104 or resid 106 through 176 or resid 178 throu \ gh 239 or resid 241 through 285 or resid 287 through 363)) selection = (chain 'D' and (resid 28 through 104 or resid 106 through 176 or resid 178 throu \ gh 239 or resid 241 through 285 or resid 287 through 363)) } 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=0.21 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: 0.760 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: 4.170 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.910 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12334 Z= 0.225 Angle : 0.598 13.671 16741 Z= 0.298 Chirality : 0.044 0.237 1881 Planarity : 0.004 0.051 2151 Dihedral : 14.458 90.785 4691 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1507 helix: -0.14 (0.21), residues: 611 sheet: 2.00 (0.40), residues: 185 loop : -0.66 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.008 0.001 HIS B 289 PHE 0.014 0.001 PHE C 355 TYR 0.013 0.001 TYR B 221 ARG 0.003 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.449 Fit side-chains REVERT: A 359 MET cc_start: 0.7538 (tpt) cc_final: 0.7328 (tpt) REVERT: B 251 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7679 (mptt) REVERT: B 252 ASN cc_start: 0.8136 (m-40) cc_final: 0.7888 (m-40) REVERT: C 86 ASP cc_start: 0.7987 (m-30) cc_final: 0.7344 (p0) REVERT: E 141 MET cc_start: 0.4947 (ptm) cc_final: 0.4626 (pmt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 1.7024 time to fit residues: 266.5925 Evaluate side-chains 114 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.0020 chunk 88 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN E 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12334 Z= 0.292 Angle : 0.561 13.571 16741 Z= 0.286 Chirality : 0.045 0.143 1881 Planarity : 0.005 0.045 2151 Dihedral : 10.308 83.913 1885 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.41 % Allowed : 5.71 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1507 helix: -0.37 (0.21), residues: 627 sheet: 1.79 (0.40), residues: 179 loop : -0.70 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.009 0.002 HIS D 289 PHE 0.023 0.002 PHE C 355 TYR 0.016 0.002 TYR C 221 ARG 0.003 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.284 Fit side-chains REVERT: B 157 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: B 251 LYS cc_start: 0.7893 (mmtm) cc_final: 0.7645 (mptt) REVERT: C 86 ASP cc_start: 0.7962 (m-30) cc_final: 0.7719 (m-30) REVERT: C 363 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.5930 (mpm) REVERT: D 251 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8335 (mtmt) REVERT: E 141 MET cc_start: 0.5063 (ptm) cc_final: 0.4650 (pmt) outliers start: 18 outliers final: 9 residues processed: 130 average time/residue: 1.7311 time to fit residues: 239.8439 Evaluate side-chains 127 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.0980 chunk 114 optimal weight: 0.0050 chunk 93 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 148 optimal weight: 30.0000 chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 252 ASN B 292 ASN B 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12334 Z= 0.196 Angle : 0.503 11.618 16741 Z= 0.256 Chirality : 0.043 0.141 1881 Planarity : 0.004 0.045 2151 Dihedral : 8.388 71.261 1885 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.02 % Allowed : 6.96 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1507 helix: -0.30 (0.21), residues: 628 sheet: 1.80 (0.41), residues: 179 loop : -0.67 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.006 0.001 HIS B 289 PHE 0.017 0.001 PHE C 355 TYR 0.013 0.001 TYR C 221 ARG 0.009 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.355 Fit side-chains REVERT: B 251 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7618 (mptt) REVERT: C 86 ASP cc_start: 0.7965 (m-30) cc_final: 0.7717 (m-30) outliers start: 13 outliers final: 8 residues processed: 125 average time/residue: 1.7139 time to fit residues: 228.1016 Evaluate side-chains 123 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 HIS B 252 ASN B 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 12334 Z= 0.431 Angle : 0.649 12.454 16741 Z= 0.332 Chirality : 0.049 0.152 1881 Planarity : 0.006 0.050 2151 Dihedral : 8.543 66.803 1885 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.64 % Allowed : 7.58 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.21), residues: 1507 helix: -0.58 (0.20), residues: 630 sheet: 1.53 (0.40), residues: 174 loop : -0.89 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 327 HIS 0.010 0.002 HIS B 289 PHE 0.023 0.002 PHE C 355 TYR 0.020 0.002 TYR C 221 ARG 0.006 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7798 (tpp-160) cc_final: 0.7534 (ttm110) REVERT: A 150 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 157 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: B 251 LYS cc_start: 0.7897 (mmtm) cc_final: 0.7657 (mptt) REVERT: C 86 ASP cc_start: 0.8000 (m-30) cc_final: 0.7750 (m-30) REVERT: D 251 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8332 (mtmt) outliers start: 21 outliers final: 10 residues processed: 129 average time/residue: 1.7741 time to fit residues: 243.1704 Evaluate side-chains 126 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 359 MET Chi-restraints excluded: chain D residue 360 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 292 ASN C 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12334 Z= 0.125 Angle : 0.463 11.317 16741 Z= 0.235 Chirality : 0.041 0.141 1881 Planarity : 0.004 0.045 2151 Dihedral : 7.633 64.260 1885 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.78 % Allowed : 9.07 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1507 helix: -0.34 (0.21), residues: 622 sheet: 1.74 (0.40), residues: 185 loop : -0.72 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 327 HIS 0.005 0.001 HIS B 289 PHE 0.010 0.001 PHE C 355 TYR 0.009 0.001 TYR C 221 ARG 0.010 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.326 Fit side-chains REVERT: A 32 ARG cc_start: 0.7749 (tpp-160) cc_final: 0.7503 (ttm110) REVERT: A 150 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: C 86 ASP cc_start: 0.7970 (m-30) cc_final: 0.7720 (m-30) outliers start: 10 outliers final: 6 residues processed: 118 average time/residue: 1.7439 time to fit residues: 219.1706 Evaluate side-chains 116 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 12334 Z= 0.503 Angle : 0.682 10.105 16741 Z= 0.350 Chirality : 0.050 0.155 1881 Planarity : 0.006 0.052 2151 Dihedral : 8.246 68.076 1885 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.49 % Allowed : 8.68 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1507 helix: -0.59 (0.20), residues: 624 sheet: 1.43 (0.40), residues: 174 loop : -0.90 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 327 HIS 0.010 0.002 HIS B 289 PHE 0.023 0.002 PHE C 355 TYR 0.021 0.002 TYR D 221 ARG 0.007 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.406 Fit side-chains REVERT: A 150 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 91 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6841 (mtm180) REVERT: C 86 ASP cc_start: 0.8066 (m-30) cc_final: 0.7825 (m-30) REVERT: D 251 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8350 (mtmt) outliers start: 19 outliers final: 10 residues processed: 122 average time/residue: 1.7895 time to fit residues: 232.3319 Evaluate side-chains 124 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain E residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN C 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12334 Z= 0.178 Angle : 0.508 9.374 16741 Z= 0.261 Chirality : 0.042 0.141 1881 Planarity : 0.004 0.045 2151 Dihedral : 7.757 67.204 1885 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.86 % Allowed : 9.93 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1507 helix: -0.38 (0.21), residues: 620 sheet: 1.64 (0.39), residues: 186 loop : -0.82 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.005 0.001 HIS B 289 PHE 0.014 0.001 PHE C 355 TYR 0.013 0.001 TYR C 221 ARG 0.009 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.448 Fit side-chains REVERT: A 150 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: B 157 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: C 86 ASP cc_start: 0.8034 (m-30) cc_final: 0.7798 (m-30) outliers start: 11 outliers final: 7 residues processed: 119 average time/residue: 1.8788 time to fit residues: 237.1163 Evaluate side-chains 119 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 114 optimal weight: 0.2980 chunk 132 optimal weight: 6.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12334 Z= 0.221 Angle : 0.520 10.182 16741 Z= 0.267 Chirality : 0.043 0.139 1881 Planarity : 0.005 0.045 2151 Dihedral : 7.614 66.197 1885 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.17 % Allowed : 9.70 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1507 helix: -0.31 (0.21), residues: 622 sheet: 1.64 (0.39), residues: 186 loop : -0.77 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 327 HIS 0.006 0.001 HIS B 289 PHE 0.015 0.001 PHE C 355 TYR 0.015 0.001 TYR C 221 ARG 0.009 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.314 Fit side-chains REVERT: A 32 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7559 (ttm110) REVERT: A 150 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: B 157 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: C 86 ASP cc_start: 0.8040 (m-30) cc_final: 0.7807 (m-30) outliers start: 15 outliers final: 9 residues processed: 121 average time/residue: 1.8565 time to fit residues: 238.3763 Evaluate side-chains 123 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12334 Z= 0.451 Angle : 0.659 10.563 16741 Z= 0.338 Chirality : 0.049 0.150 1881 Planarity : 0.006 0.048 2151 Dihedral : 8.081 68.449 1885 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.09 % Allowed : 9.77 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1507 helix: -0.55 (0.21), residues: 622 sheet: 1.47 (0.40), residues: 174 loop : -0.95 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 327 HIS 0.009 0.002 HIS B 289 PHE 0.022 0.002 PHE C 355 TYR 0.021 0.002 TYR C 221 ARG 0.008 0.001 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.492 Fit side-chains REVERT: A 32 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7569 (ttm110) REVERT: A 150 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 157 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: C 86 ASP cc_start: 0.8086 (m-30) cc_final: 0.7858 (m-30) REVERT: D 189 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6865 (mm-40) outliers start: 14 outliers final: 9 residues processed: 117 average time/residue: 1.8674 time to fit residues: 231.8657 Evaluate side-chains 123 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 138 optimal weight: 0.0670 chunk 119 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN C 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 12334 Z= 0.155 Angle : 0.503 11.011 16741 Z= 0.258 Chirality : 0.042 0.141 1881 Planarity : 0.004 0.046 2151 Dihedral : 7.614 67.114 1885 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.02 % Allowed : 10.09 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.21), residues: 1507 helix: -0.37 (0.21), residues: 621 sheet: 1.63 (0.40), residues: 180 loop : -0.80 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.005 0.001 HIS B 289 PHE 0.012 0.001 PHE C 355 TYR 0.011 0.001 TYR C 221 ARG 0.010 0.000 ARG C 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.254 Fit side-chains REVERT: A 32 ARG cc_start: 0.7771 (tpp-160) cc_final: 0.7542 (ttm110) REVERT: A 150 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: B 157 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: C 86 ASP cc_start: 0.8034 (m-30) cc_final: 0.7823 (m-30) outliers start: 13 outliers final: 8 residues processed: 118 average time/residue: 2.0385 time to fit residues: 255.6366 Evaluate side-chains 121 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.0070 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 123 optimal weight: 0.1980 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN D 122 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095006 restraints weight = 22133.128| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.29 r_work: 0.2932 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12334 Z= 0.113 Angle : 0.448 11.395 16741 Z= 0.225 Chirality : 0.041 0.139 1881 Planarity : 0.004 0.045 2151 Dihedral : 7.003 61.854 1885 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.55 % Allowed : 10.24 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1507 helix: -0.15 (0.21), residues: 620 sheet: 1.77 (0.39), residues: 189 loop : -0.60 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 327 HIS 0.004 0.001 HIS B 289 PHE 0.007 0.001 PHE B 312 TYR 0.008 0.001 TYR A 302 ARG 0.010 0.000 ARG C 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4591.96 seconds wall clock time: 82 minutes 14.20 seconds (4934.20 seconds total)