Starting phenix.real_space_refine on Sun Mar 17 03:24:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5r_20653/03_2024/6u5r_20653.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5r_20653/03_2024/6u5r_20653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5r_20653/03_2024/6u5r_20653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5r_20653/03_2024/6u5r_20653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5r_20653/03_2024/6u5r_20653.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5r_20653/03_2024/6u5r_20653.pdb" } resolution = 3.6 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= 0.004 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 Ca 8 9.91 5 S 68 5.16 5 C 10436 2.51 5 N 2820 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 64": "OD1" <-> "OD2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ASP 305": "OD1" <-> "OD2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ASP 305": "OD1" <-> "OD2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 64": "OD1" <-> "OD2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 64": "OD1" <-> "OD2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G ASP 245": "OD1" <-> "OD2" Residue "G GLU 248": "OE1" <-> "OE2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G GLU 301": "OE1" <-> "OE2" Residue "G ASP 305": "OD1" <-> "OD2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H ASP 184": "OD1" <-> "OD2" Residue "H ARG 199": "NH1" <-> "NH2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 263": "NH1" <-> "NH2" Residue "H ASP 305": "OD1" <-> "OD2" Residue "H PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16516 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2445 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2445 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2445 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2445 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.01, per 1000 atoms: 0.55 Number of scatterers: 16516 At special positions: 0 Unit cell: (150.152, 150.152, 117.272, 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) Ca 8 19.99 S 68 16.00 O 3184 8.00 N 2820 7.00 C 10436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.40 Conformation dependent library (CDL) restraints added in 3.2 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 46.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 removed outlier: 3.920A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 69 through 105 removed outlier: 4.076A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.530A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.755A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.604A pdb=" N ILE A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 removed outlier: 4.044A pdb=" N MET A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.692A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.359A pdb=" N LYS B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.578A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.662A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.709A pdb=" N PHE B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.924A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 42 removed outlier: 3.920A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 69 through 105 removed outlier: 4.076A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 3.530A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.755A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.604A pdb=" N ILE C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 removed outlier: 4.044A pdb=" N MET C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 251 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 335 removed outlier: 3.692A pdb=" N SER C 335 " --> pdb=" O LYS C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.360A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.578A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 240 removed outlier: 3.662A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.709A pdb=" N PHE D 251 " --> pdb=" O TYR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.924A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 42 removed outlier: 3.920A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 69 through 105 removed outlier: 4.076A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 3.530A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.754A pdb=" N THR E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 223 Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.604A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 257 removed outlier: 4.043A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 323 through 335 removed outlier: 3.691A pdb=" N SER E 335 " --> pdb=" O LYS E 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 146 through 156 removed outlier: 4.359A pdb=" N LYS F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.579A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.661A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.710A pdb=" N PHE F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.924A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 42 removed outlier: 3.920A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 69 through 105 removed outlier: 4.077A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL G 91 " --> pdb=" O PHE G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 3.530A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 170 Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.755A pdb=" N THR G 191 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 223 Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.604A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 257 removed outlier: 4.043A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE G 251 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 323 through 335 removed outlier: 3.692A pdb=" N SER G 335 " --> pdb=" O LYS G 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 146 through 156 removed outlier: 4.359A pdb=" N LYS H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.577A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.662A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 removed outlier: 3.710A pdb=" N PHE H 251 " --> pdb=" O TYR H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.925A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.493A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 207 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE A 229 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA A 209 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.296A pdb=" N ILE A 317 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 296 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 296 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 161 removed outlier: 7.221A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 229 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.554A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.493A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 207 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE C 229 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA C 209 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.296A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 296 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 160 through 161 removed outlier: 7.221A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 229 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.554A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.492A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA E 209 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.296A pdb=" N ILE E 317 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL E 296 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU E 319 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 296 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 160 through 161 removed outlier: 7.221A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE F 229 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.554A pdb=" N GLY F 295 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.494A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE G 229 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA G 209 " --> pdb=" O ILE G 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.297A pdb=" N ILE G 317 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL G 296 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU G 319 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL G 296 " --> pdb=" O ILE G 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 160 through 161 removed outlier: 7.222A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE H 229 " --> pdb=" O ALA H 209 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.554A pdb=" N GLY H 295 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2064 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: 5.09 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4147 1.33 - 1.45: 2871 1.45 - 1.57: 9610 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 16740 Sorted by residual: bond pdb=" CG1 ILE G 195 " pdb=" CD1 ILE G 195 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.35e+00 bond pdb=" CG1 ILE A 195 " pdb=" CD1 ILE A 195 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.35e+00 bond pdb=" CG1 ILE E 195 " pdb=" CD1 ILE E 195 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.35e+00 bond pdb=" CG1 ILE C 195 " pdb=" CD1 ILE C 195 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.35e+00 bond pdb=" CG LEU F 220 " pdb=" CD2 LEU F 220 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.15e+00 ... (remaining 16735 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.65: 268 105.65 - 112.75: 9022 112.75 - 119.85: 6219 119.85 - 126.95: 7043 126.95 - 134.05: 132 Bond angle restraints: 22684 Sorted by residual: angle pdb=" C GLY D 299 " pdb=" N ASP D 300 " pdb=" CA ASP D 300 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C GLY F 299 " pdb=" N ASP F 300 " pdb=" CA ASP F 300 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C GLY B 299 " pdb=" N ASP B 300 " pdb=" CA ASP B 300 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C GLY H 299 " pdb=" N ASP H 300 " pdb=" CA ASP H 300 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C GLY A 272 " pdb=" N SER A 273 " pdb=" CA SER A 273 " ideal model delta sigma weight residual 123.05 128.31 -5.26 1.57e+00 4.06e-01 1.12e+01 ... (remaining 22679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 8940 16.71 - 33.41: 924 33.41 - 50.12: 224 50.12 - 66.82: 24 66.82 - 83.53: 12 Dihedral angle restraints: 10124 sinusoidal: 3972 harmonic: 6152 Sorted by residual: dihedral pdb=" CA SER E 273 " pdb=" C SER E 273 " pdb=" N LYS E 274 " pdb=" CA LYS E 274 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER G 273 " pdb=" C SER G 273 " pdb=" N LYS G 274 " pdb=" CA LYS G 274 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER A 273 " pdb=" C SER A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 10121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1472 0.048 - 0.095: 926 0.095 - 0.143: 250 0.143 - 0.191: 28 0.191 - 0.238: 12 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA ASP D 300 " pdb=" N ASP D 300 " pdb=" C ASP D 300 " pdb=" CB ASP D 300 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP F 300 " pdb=" N ASP F 300 " pdb=" C ASP F 300 " pdb=" CB ASP F 300 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ASP H 300 " pdb=" N ASP H 300 " pdb=" C ASP H 300 " pdb=" CB ASP H 300 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2685 not shown) Planarity restraints: 2932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 252 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C VAL G 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL G 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN G 253 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 252 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C VAL A 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL A 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 253 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 252 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C VAL C 252 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL C 252 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN C 253 " -0.011 2.00e-02 2.50e+03 ... (remaining 2929 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 51 2.39 - 3.02: 8640 3.02 - 3.65: 23709 3.65 - 4.27: 34898 4.27 - 4.90: 59912 Nonbonded interactions: 127210 Sorted by model distance: nonbonded pdb="CA CA H 401 " pdb=" O HOH H 501 " model vdw 1.768 2.510 nonbonded pdb="CA CA B 401 " pdb=" O HOH B 501 " model vdw 1.768 2.510 nonbonded pdb="CA CA F 401 " pdb=" O HOH F 501 " model vdw 1.768 2.510 nonbonded pdb="CA CA D 401 " pdb=" O HOH D 501 " model vdw 1.768 2.510 nonbonded pdb=" OD2 ASP H 184 " pdb=" OE1 GLU H 210 " model vdw 2.206 3.040 ... (remaining 127205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.010 Extract box with map and model: 3.520 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 43.740 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.011 0.090 16740 Z= 0.701 Angle : 0.960 10.280 22684 Z= 0.550 Chirality : 0.061 0.238 2688 Planarity : 0.005 0.043 2932 Dihedral : 14.543 83.528 6172 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.23 % Allowed : 12.44 % Favored : 87.33 % 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: -4.18 (0.13), residues: 2140 helix: -3.07 (0.11), residues: 992 sheet: -0.44 (0.26), residues: 344 loop : -3.26 (0.15), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 123 HIS 0.018 0.003 HIS E 117 PHE 0.021 0.003 PHE B 232 TYR 0.013 0.002 TYR F 214 ARG 0.005 0.001 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 466 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8612 (tmmt) cc_final: 0.8404 (tmmt) REVERT: A 200 LYS cc_start: 0.8564 (tptm) cc_final: 0.8266 (tppt) REVERT: A 218 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6395 (mm-30) REVERT: A 264 MET cc_start: 0.8408 (ttm) cc_final: 0.8177 (ttt) REVERT: B 250 MET cc_start: 0.8711 (mtt) cc_final: 0.8454 (mtt) REVERT: B 301 GLU cc_start: 0.7097 (pp20) cc_final: 0.6337 (pp20) REVERT: C 105 LYS cc_start: 0.8614 (tmmt) cc_final: 0.8403 (tmmt) REVERT: C 200 LYS cc_start: 0.8574 (tptm) cc_final: 0.8318 (tptm) REVERT: C 218 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6386 (mm-30) REVERT: C 264 MET cc_start: 0.8421 (ttm) cc_final: 0.8182 (ttt) REVERT: D 250 MET cc_start: 0.8708 (mtt) cc_final: 0.8450 (mtt) REVERT: D 301 GLU cc_start: 0.7101 (pp20) cc_final: 0.6347 (pp20) REVERT: E 105 LYS cc_start: 0.8615 (tmmt) cc_final: 0.8405 (tmmt) REVERT: E 200 LYS cc_start: 0.8576 (tptm) cc_final: 0.8321 (tptm) REVERT: E 218 GLU cc_start: 0.6610 (mm-30) cc_final: 0.6398 (mm-30) REVERT: E 264 MET cc_start: 0.8408 (ttm) cc_final: 0.8183 (ttt) REVERT: F 250 MET cc_start: 0.8710 (mtt) cc_final: 0.8449 (mtt) REVERT: F 301 GLU cc_start: 0.7105 (pp20) cc_final: 0.6273 (pp20) REVERT: G 105 LYS cc_start: 0.8612 (tmmt) cc_final: 0.8400 (tmmt) REVERT: G 200 LYS cc_start: 0.8572 (tptm) cc_final: 0.8314 (tptm) REVERT: G 218 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6406 (mm-30) REVERT: G 264 MET cc_start: 0.8406 (ttm) cc_final: 0.8176 (ttt) REVERT: H 250 MET cc_start: 0.8709 (mtt) cc_final: 0.8450 (mtt) REVERT: H 301 GLU cc_start: 0.7094 (pp20) cc_final: 0.6335 (pp20) outliers start: 4 outliers final: 4 residues processed: 470 average time/residue: 0.3654 time to fit residues: 234.1823 Evaluate side-chains 344 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 340 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain G residue 64 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 219 GLN A 253 GLN B 147 ASN C 103 GLN C 219 GLN C 253 GLN D 147 ASN E 103 GLN E 219 GLN E 253 GLN F 147 ASN G 103 GLN G 219 GLN G 253 GLN H 147 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16740 Z= 0.190 Angle : 0.528 7.601 22684 Z= 0.282 Chirality : 0.045 0.152 2688 Planarity : 0.003 0.027 2932 Dihedral : 5.107 50.000 2364 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.53 % Allowed : 18.24 % Favored : 79.22 % 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: -2.54 (0.16), residues: 2140 helix: -1.16 (0.15), residues: 1008 sheet: -0.20 (0.26), residues: 336 loop : -2.98 (0.16), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 52 HIS 0.004 0.001 HIS A 117 PHE 0.009 0.001 PHE A 75 TYR 0.020 0.001 TYR A 333 ARG 0.003 0.000 ARG F 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 405 time to evaluate : 1.784 Fit side-chains REVERT: A 105 LYS cc_start: 0.8531 (tmmt) cc_final: 0.8282 (tmmt) REVERT: B 179 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7619 (tpt-90) REVERT: B 323 LYS cc_start: 0.8148 (mttp) cc_final: 0.7895 (mtpp) REVERT: C 105 LYS cc_start: 0.8532 (tmmt) cc_final: 0.8285 (tmmt) REVERT: D 179 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7619 (tpt-90) REVERT: D 323 LYS cc_start: 0.8146 (mttp) cc_final: 0.7891 (mtpp) REVERT: E 105 LYS cc_start: 0.8535 (tmmt) cc_final: 0.8285 (tmmt) REVERT: F 179 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7636 (tpt-90) REVERT: F 323 LYS cc_start: 0.8177 (mttp) cc_final: 0.7912 (mtpp) REVERT: G 105 LYS cc_start: 0.8532 (tmmt) cc_final: 0.8281 (tmmt) REVERT: H 179 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7617 (tpt-90) REVERT: H 323 LYS cc_start: 0.8150 (mttp) cc_final: 0.7901 (mtpp) outliers start: 45 outliers final: 16 residues processed: 438 average time/residue: 0.3475 time to fit residues: 212.8155 Evaluate side-chains 349 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 333 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 0.0030 chunk 53 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 ASN C 103 GLN D 147 ASN E 103 GLN F 147 ASN H 147 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16740 Z= 0.243 Angle : 0.540 7.957 22684 Z= 0.280 Chirality : 0.047 0.184 2688 Planarity : 0.004 0.070 2932 Dihedral : 4.755 49.611 2356 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.60 % Allowed : 21.57 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2140 helix: -0.21 (0.16), residues: 1008 sheet: 0.11 (0.27), residues: 336 loop : -2.75 (0.17), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 52 HIS 0.006 0.001 HIS E 117 PHE 0.006 0.001 PHE A 75 TYR 0.016 0.001 TYR C 333 ARG 0.007 0.000 ARG H 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 359 time to evaluate : 1.879 Fit side-chains REVERT: B 179 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7652 (tpt-90) REVERT: B 323 LYS cc_start: 0.8198 (mttp) cc_final: 0.7837 (mtpp) REVERT: D 179 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7650 (tpt-90) REVERT: D 323 LYS cc_start: 0.8209 (mttp) cc_final: 0.7838 (mtpp) REVERT: F 179 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7652 (tpt-90) REVERT: F 323 LYS cc_start: 0.8211 (mttp) cc_final: 0.7846 (mtpp) REVERT: H 179 ARG cc_start: 0.8004 (mtp180) cc_final: 0.7638 (tpt-90) REVERT: H 323 LYS cc_start: 0.8211 (mttp) cc_final: 0.7849 (mtpp) outliers start: 64 outliers final: 35 residues processed: 399 average time/residue: 0.3473 time to fit residues: 193.3360 Evaluate side-chains 371 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 336 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 261 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN E 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16740 Z= 0.192 Angle : 0.498 7.881 22684 Z= 0.258 Chirality : 0.046 0.166 2688 Planarity : 0.003 0.050 2932 Dihedral : 4.448 48.281 2356 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.77 % Allowed : 22.97 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2140 helix: 0.30 (0.17), residues: 1020 sheet: 0.33 (0.27), residues: 336 loop : -2.48 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 52 HIS 0.004 0.001 HIS F 117 PHE 0.007 0.001 PHE E 75 TYR 0.010 0.001 TYR F 214 ARG 0.007 0.000 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 363 time to evaluate : 2.120 Fit side-chains REVERT: A 333 TYR cc_start: 0.8743 (t80) cc_final: 0.8468 (t80) REVERT: B 179 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7661 (tpt-90) REVERT: B 323 LYS cc_start: 0.8154 (mttp) cc_final: 0.7792 (mtpp) REVERT: C 333 TYR cc_start: 0.8740 (t80) cc_final: 0.8464 (t80) REVERT: D 179 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7661 (tpt-90) REVERT: D 323 LYS cc_start: 0.8170 (mttp) cc_final: 0.7806 (mtpp) REVERT: E 333 TYR cc_start: 0.8735 (t80) cc_final: 0.8458 (t80) REVERT: F 179 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7656 (tpt-90) REVERT: F 323 LYS cc_start: 0.8084 (mttp) cc_final: 0.7792 (mtpp) REVERT: G 333 TYR cc_start: 0.8742 (t80) cc_final: 0.8463 (t80) REVERT: H 179 ARG cc_start: 0.8011 (mtp180) cc_final: 0.7656 (tpt-90) REVERT: H 323 LYS cc_start: 0.8175 (mttp) cc_final: 0.7812 (mtpp) outliers start: 67 outliers final: 51 residues processed: 409 average time/residue: 0.3482 time to fit residues: 199.1143 Evaluate side-chains 370 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 319 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 174 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 183 optimal weight: 0.0970 chunk 51 optimal weight: 7.9990 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 253 GLN C 103 GLN C 253 GLN E 103 GLN G 103 GLN G 253 GLN H 147 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16740 Z= 0.235 Angle : 0.515 7.504 22684 Z= 0.266 Chirality : 0.046 0.143 2688 Planarity : 0.003 0.046 2932 Dihedral : 4.336 47.742 2356 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.67 % Allowed : 25.11 % Favored : 70.21 % 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: -0.77 (0.18), residues: 2140 helix: 0.59 (0.17), residues: 1020 sheet: 0.37 (0.28), residues: 332 loop : -2.43 (0.18), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 52 HIS 0.004 0.001 HIS A 117 PHE 0.006 0.001 PHE C 75 TYR 0.010 0.001 TYR D 214 ARG 0.008 0.000 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 352 time to evaluate : 1.810 Fit side-chains REVERT: A 105 LYS cc_start: 0.8599 (tmmt) cc_final: 0.8306 (tmmt) REVERT: B 179 ARG cc_start: 0.8027 (mtp180) cc_final: 0.7669 (tpt-90) REVERT: B 323 LYS cc_start: 0.8134 (mttp) cc_final: 0.7849 (mtpp) REVERT: C 105 LYS cc_start: 0.8601 (tmmt) cc_final: 0.8310 (tmmt) REVERT: D 179 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7671 (tpt-90) REVERT: E 105 LYS cc_start: 0.8608 (tmmt) cc_final: 0.8312 (tmmt) REVERT: F 179 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7687 (tpt-90) REVERT: F 323 LYS cc_start: 0.8149 (mttp) cc_final: 0.7869 (mtpp) REVERT: G 105 LYS cc_start: 0.8603 (tmmt) cc_final: 0.8306 (tmmt) REVERT: H 179 ARG cc_start: 0.8027 (mtp180) cc_final: 0.7665 (tpt-90) REVERT: H 323 LYS cc_start: 0.8141 (mttp) cc_final: 0.7856 (mtpp) outliers start: 83 outliers final: 59 residues processed: 403 average time/residue: 0.3419 time to fit residues: 192.3950 Evaluate side-chains 381 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 322 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.6980 chunk 184 optimal weight: 0.0030 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 0.0000 chunk 205 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 103 GLN E 103 GLN E 253 GLN G 103 GLN H 147 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16740 Z= 0.122 Angle : 0.478 8.522 22684 Z= 0.241 Chirality : 0.045 0.165 2688 Planarity : 0.003 0.041 2932 Dihedral : 4.027 43.590 2356 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.77 % Allowed : 25.68 % Favored : 70.55 % 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: -0.41 (0.18), residues: 2140 helix: 0.85 (0.17), residues: 1028 sheet: 0.67 (0.28), residues: 332 loop : -2.29 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 52 HIS 0.002 0.001 HIS B 117 PHE 0.007 0.001 PHE C 75 TYR 0.008 0.001 TYR F 310 ARG 0.008 0.000 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 353 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 TYR cc_start: 0.8516 (t80) cc_final: 0.8285 (t80) REVERT: B 179 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7596 (tpt-90) REVERT: C 333 TYR cc_start: 0.8515 (t80) cc_final: 0.8284 (t80) REVERT: D 179 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7595 (tpt-90) REVERT: E 105 LYS cc_start: 0.8582 (tmmt) cc_final: 0.8275 (tmmt) REVERT: E 333 TYR cc_start: 0.8508 (t80) cc_final: 0.8283 (t80) REVERT: F 179 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7607 (tpt-90) REVERT: G 333 TYR cc_start: 0.8512 (t80) cc_final: 0.8281 (t80) REVERT: H 179 ARG cc_start: 0.7938 (mtp180) cc_final: 0.7592 (tpt-90) outliers start: 67 outliers final: 53 residues processed: 394 average time/residue: 0.3310 time to fit residues: 183.5445 Evaluate side-chains 384 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 331 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 116 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 0.4980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN C 216 ASN E 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16740 Z= 0.123 Angle : 0.460 10.426 22684 Z= 0.233 Chirality : 0.045 0.206 2688 Planarity : 0.003 0.041 2932 Dihedral : 3.790 39.536 2356 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.17 % Allowed : 25.06 % Favored : 70.78 % 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: -0.01 (0.18), residues: 2140 helix: 1.18 (0.17), residues: 1020 sheet: 0.87 (0.29), residues: 332 loop : -2.06 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 52 HIS 0.002 0.000 HIS B 117 PHE 0.006 0.001 PHE G 75 TYR 0.008 0.001 TYR D 310 ARG 0.006 0.000 ARG H 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 341 time to evaluate : 1.918 Fit side-chains REVERT: A 105 LYS cc_start: 0.8557 (tmmt) cc_final: 0.8279 (tmmt) REVERT: A 333 TYR cc_start: 0.8457 (t80) cc_final: 0.8218 (t80) REVERT: C 105 LYS cc_start: 0.8566 (tmmt) cc_final: 0.8281 (tmmt) REVERT: E 105 LYS cc_start: 0.8574 (tmmt) cc_final: 0.8325 (tmmt) REVERT: E 333 TYR cc_start: 0.8455 (t80) cc_final: 0.8216 (t80) REVERT: G 105 LYS cc_start: 0.8565 (tmmt) cc_final: 0.8278 (tmmt) outliers start: 74 outliers final: 53 residues processed: 388 average time/residue: 0.3462 time to fit residues: 185.9877 Evaluate side-chains 378 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 325 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 185 optimal weight: 0.2980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16740 Z= 0.159 Angle : 0.465 8.833 22684 Z= 0.236 Chirality : 0.045 0.132 2688 Planarity : 0.003 0.040 2932 Dihedral : 3.758 38.055 2356 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.17 % Allowed : 24.94 % Favored : 70.89 % 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: 0.09 (0.18), residues: 2140 helix: 1.26 (0.17), residues: 1020 sheet: 0.94 (0.29), residues: 332 loop : -2.03 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 52 HIS 0.003 0.001 HIS F 117 PHE 0.008 0.001 PHE E 75 TYR 0.008 0.001 TYR H 310 ARG 0.009 0.000 ARG H 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 341 time to evaluate : 1.921 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8599 (tmmt) cc_final: 0.8341 (tmmt) REVERT: A 333 TYR cc_start: 0.8481 (t80) cc_final: 0.8234 (t80) REVERT: C 105 LYS cc_start: 0.8598 (tmmt) cc_final: 0.8342 (tmmt) REVERT: C 333 TYR cc_start: 0.8470 (t80) cc_final: 0.8231 (t80) REVERT: E 105 LYS cc_start: 0.8642 (tmmt) cc_final: 0.8377 (tmmt) REVERT: E 333 TYR cc_start: 0.8475 (t80) cc_final: 0.8228 (t80) REVERT: G 105 LYS cc_start: 0.8598 (tmmt) cc_final: 0.8338 (tmmt) REVERT: G 333 TYR cc_start: 0.8465 (t80) cc_final: 0.8228 (t80) outliers start: 74 outliers final: 66 residues processed: 389 average time/residue: 0.3421 time to fit residues: 185.6222 Evaluate side-chains 388 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 322 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 130 CYS Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 130 CYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.0944 > 50: distance: 48 - 54: 4.873 distance: 54 - 55: 12.116 distance: 54 - 60: 24.290 distance: 55 - 56: 12.018 distance: 55 - 58: 17.949 distance: 56 - 57: 12.364 distance: 56 - 61: 13.981 distance: 58 - 59: 20.754 distance: 59 - 60: 32.975 distance: 61 - 62: 7.836 distance: 62 - 63: 9.321 distance: 63 - 64: 5.014 distance: 63 - 68: 4.802 distance: 65 - 66: 12.696 distance: 65 - 67: 11.925 distance: 68 - 69: 8.761 distance: 69 - 72: 9.668 distance: 70 - 71: 18.321 distance: 70 - 79: 9.183 distance: 72 - 73: 11.211 distance: 73 - 74: 8.983 distance: 74 - 75: 14.287 distance: 75 - 76: 7.588 distance: 76 - 77: 21.592 distance: 76 - 78: 17.940 distance: 79 - 80: 7.033 distance: 80 - 81: 7.871 distance: 80 - 83: 12.801 distance: 81 - 82: 4.214 distance: 81 - 86: 14.811 distance: 83 - 84: 21.210 distance: 83 - 85: 6.256 distance: 86 - 87: 9.438 distance: 87 - 88: 16.053 distance: 87 - 90: 9.478 distance: 88 - 89: 8.456 distance: 88 - 92: 11.744 distance: 90 - 91: 17.609 distance: 92 - 93: 5.806 distance: 93 - 94: 26.008 distance: 93 - 96: 6.327 distance: 94 - 95: 25.996 distance: 94 - 100: 9.332 distance: 96 - 97: 10.380 distance: 97 - 98: 11.239 distance: 97 - 99: 11.200 distance: 100 - 101: 11.007 distance: 101 - 102: 32.146 distance: 101 - 104: 9.023 distance: 102 - 103: 43.238 distance: 102 - 108: 29.221 distance: 104 - 105: 22.421 distance: 105 - 106: 15.864 distance: 105 - 107: 15.886 distance: 108 - 109: 12.310 distance: 109 - 110: 27.100 distance: 109 - 112: 18.307 distance: 110 - 111: 18.483 distance: 110 - 117: 12.176 distance: 112 - 113: 25.724 distance: 113 - 114: 8.619 distance: 114 - 115: 24.959 distance: 114 - 116: 9.004 distance: 117 - 118: 3.062 distance: 118 - 119: 10.314 distance: 118 - 121: 11.221 distance: 119 - 120: 4.992 distance: 119 - 126: 6.541 distance: 121 - 122: 15.079 distance: 122 - 123: 5.851 distance: 123 - 124: 14.228 distance: 124 - 125: 25.168 distance: 126 - 127: 7.864 distance: 127 - 128: 6.724 distance: 127 - 130: 8.828 distance: 128 - 129: 17.399 distance: 128 - 131: 3.245