Starting phenix.real_space_refine on Sat Mar 23 20:37:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/03_2024/7tu5_26126.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/03_2024/7tu5_26126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/03_2024/7tu5_26126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/03_2024/7tu5_26126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/03_2024/7tu5_26126.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/03_2024/7tu5_26126.pdb" } resolution = 2.1 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= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19206 atoms to isotropic. 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 Mg 6 5.21 5 S 42 5.16 5 C 12624 2.51 5 N 3396 2.21 5 O 3588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 104": "OD1" <-> "OD2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F ARG 142": "NH1" <-> "NH2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F PHE 334": "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: 19656 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3274 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "B" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3274 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "C" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3274 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "D" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3274 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "E" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3274 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "F" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3274 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 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} Time building chain proxies: 10.12, per 1000 atoms: 0.51 Number of scatterers: 19656 At special positions: 0 Unit cell: (125.97, 133.722, 98.838, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 Mg 6 11.99 O 3588 8.00 N 3396 7.00 C 12624 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: 7.66 Conformation dependent library (CDL) restraints added in 3.5 seconds 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 75.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 64 through 91 Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 removed outlier: 3.650A pdb=" N ARG A 142 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 147 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.516A pdb=" N ASN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS A 208 " --> pdb=" O ILE A 205 " (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 228 Processing helix chain 'A' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 298 through 325 Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 411 through 425 Processing helix chain 'A' and resid 427 through 439 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.769A pdb=" N TYR B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 64 through 91 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.631A pdb=" N PHE B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.649A pdb=" N ARG B 142 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B 145 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 147 " --> pdb=" O LYS B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.515A pdb=" N ASN B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS B 208 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 248 " --> pdb=" O PRO B 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 298 through 325 Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 389 removed outlier: 3.715A pdb=" N GLU B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 411 through 425 Processing helix chain 'B' and resid 427 through 439 Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 47 through 50 Processing helix chain 'C' and resid 64 through 91 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 147 removed outlier: 3.650A pdb=" N ARG C 142 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 145 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 147 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.516A pdb=" N ASN C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS C 208 " --> pdb=" O ILE C 205 " (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 228 Processing helix chain 'C' and resid 243 through 268 removed outlier: 3.761A pdb=" N TYR C 247 " --> pdb=" O HIS C 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP C 261 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU C 283 " --> pdb=" O TYR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 298 through 325 Processing helix chain 'C' and resid 325 through 332 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'C' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 439 Processing helix chain 'D' and resid 4 through 8 Processing helix chain 'D' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 64 through 91 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 147 removed outlier: 3.649A pdb=" N ARG D 142 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP D 145 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 147 " --> pdb=" O LYS D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.515A pdb=" N ASN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.687A pdb=" N LYS D 208 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 228 Processing helix chain 'D' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR D 247 " --> pdb=" O HIS D 243 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 248 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 261 " --> pdb=" O TYR D 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA D 276 " --> pdb=" O PRO D 272 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU D 283 " --> pdb=" O TYR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 298 through 325 Processing helix chain 'D' and resid 325 through 332 Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 344 through 359 Processing helix chain 'D' and resid 362 through 389 removed outlier: 3.715A pdb=" N GLU D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 411 through 425 Processing helix chain 'D' and resid 427 through 439 Processing helix chain 'E' and resid 4 through 8 Processing helix chain 'E' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 47 through 50 Processing helix chain 'E' and resid 64 through 91 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 135 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 147 removed outlier: 3.650A pdb=" N ARG E 142 " --> pdb=" O TYR E 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP E 145 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 147 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.516A pdb=" N ASN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'E' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS E 208 " --> pdb=" O ILE E 205 " (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 228 Processing helix chain 'E' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR E 247 " --> pdb=" O HIS E 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU E 248 " --> pdb=" O PRO E 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP E 261 " --> pdb=" O TYR E 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA E 276 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 298 through 325 Processing helix chain 'E' and resid 325 through 332 Processing helix chain 'E' and resid 338 through 342 Processing helix chain 'E' and resid 344 through 359 Processing helix chain 'E' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 403 Processing helix chain 'E' and resid 411 through 425 Processing helix chain 'E' and resid 427 through 439 Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 64 through 91 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU F 128 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE F 135 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 removed outlier: 3.649A pdb=" N ARG F 142 " --> pdb=" O TYR F 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP F 145 " --> pdb=" O ARG F 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 147 " --> pdb=" O LYS F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.515A pdb=" N ASN F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'F' and resid 204 through 208 removed outlier: 3.687A pdb=" N LYS F 208 " --> pdb=" O ILE F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 228 Processing helix chain 'F' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR F 247 " --> pdb=" O HIS F 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU F 248 " --> pdb=" O PRO F 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP F 261 " --> pdb=" O TYR F 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 285 removed outlier: 4.191A pdb=" N ALA F 276 " --> pdb=" O PRO F 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU F 283 " --> pdb=" O TYR F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 298 through 325 Processing helix chain 'F' and resid 325 through 332 Processing helix chain 'F' and resid 338 through 342 Processing helix chain 'F' and resid 344 through 359 Processing helix chain 'F' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU F 374 " --> pdb=" O ILE F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 403 Processing helix chain 'F' and resid 411 through 425 Processing helix chain 'F' and resid 427 through 439 1237 hydrogen bonds defined for protein. 3567 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: 5.89 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3192 1.29 - 1.42: 5292 1.42 - 1.55: 11459 1.55 - 1.68: 19 1.68 - 1.81: 66 Bond restraints: 20028 Sorted by residual: bond pdb=" C ARG B 77 " pdb=" O ARG B 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.29e+01 bond pdb=" C ARG E 77 " pdb=" O ARG E 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.28e+01 bond pdb=" C ARG C 77 " pdb=" O ARG C 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.27e+01 bond pdb=" C ARG F 77 " pdb=" O ARG F 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.26e+01 bond pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.26e+01 ... (remaining 20023 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.16: 477 107.16 - 113.86: 11093 113.86 - 120.55: 8347 120.55 - 127.25: 7062 127.25 - 133.95: 129 Bond angle restraints: 27108 Sorted by residual: angle pdb=" N HIS E 63 " pdb=" CA HIS E 63 " pdb=" C HIS E 63 " ideal model delta sigma weight residual 110.10 119.37 -9.27 1.49e+00 4.50e-01 3.87e+01 angle pdb=" N HIS A 63 " pdb=" CA HIS A 63 " pdb=" C HIS A 63 " ideal model delta sigma weight residual 110.10 119.35 -9.25 1.49e+00 4.50e-01 3.85e+01 angle pdb=" N HIS C 63 " pdb=" CA HIS C 63 " pdb=" C HIS C 63 " ideal model delta sigma weight residual 110.10 119.33 -9.23 1.49e+00 4.50e-01 3.84e+01 angle pdb=" N HIS B 63 " pdb=" CA HIS B 63 " pdb=" C HIS B 63 " ideal model delta sigma weight residual 110.10 119.33 -9.23 1.49e+00 4.50e-01 3.84e+01 angle pdb=" N HIS D 63 " pdb=" CA HIS D 63 " pdb=" C HIS D 63 " ideal model delta sigma weight residual 110.10 119.32 -9.22 1.49e+00 4.50e-01 3.83e+01 ... (remaining 27103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 10464 17.18 - 34.36: 1086 34.36 - 51.55: 288 51.55 - 68.73: 78 68.73 - 85.91: 24 Dihedral angle restraints: 11940 sinusoidal: 4446 harmonic: 7494 Sorted by residual: dihedral pdb=" C ILE F 260 " pdb=" N ILE F 260 " pdb=" CA ILE F 260 " pdb=" CB ILE F 260 " ideal model delta harmonic sigma weight residual -122.00 -134.51 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C ILE B 260 " pdb=" N ILE B 260 " pdb=" CA ILE B 260 " pdb=" CB ILE B 260 " ideal model delta harmonic sigma weight residual -122.00 -134.51 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C ILE A 260 " pdb=" N ILE A 260 " pdb=" CA ILE A 260 " pdb=" CB ILE A 260 " ideal model delta harmonic sigma weight residual -122.00 -134.50 12.50 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 11937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2824 0.091 - 0.183: 181 0.183 - 0.274: 31 0.274 - 0.366: 26 0.366 - 0.457: 16 Chirality restraints: 3078 Sorted by residual: chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CA ILE F 260 " pdb=" N ILE F 260 " pdb=" C ILE F 260 " pdb=" CB ILE F 260 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CA ILE A 260 " pdb=" N ILE A 260 " pdb=" C ILE A 260 " pdb=" CB ILE A 260 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 3075 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 259 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ILE F 259 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE F 259 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE F 260 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 259 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C ILE D 259 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE D 259 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE D 260 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 259 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C ILE B 259 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE B 259 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE B 260 " -0.017 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 54 2.51 - 3.11: 14099 3.11 - 3.70: 30873 3.70 - 4.30: 45208 4.30 - 4.90: 76609 Nonbonded interactions: 166843 Sorted by model distance: nonbonded pdb=" NE2 HIS C 116 " pdb="MG MG C 601 " model vdw 1.910 2.250 nonbonded pdb=" NE2 HIS B 116 " pdb="MG MG B 601 " model vdw 1.910 2.250 nonbonded pdb=" NE2 HIS D 116 " pdb="MG MG D 601 " model vdw 1.911 2.250 nonbonded pdb=" NE2 HIS E 116 " pdb="MG MG E 601 " model vdw 1.911 2.250 nonbonded pdb=" NE2 HIS A 116 " pdb="MG MG A 601 " model vdw 1.911 2.250 ... (remaining 166838 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.010 Extract box with map and model: 11.130 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 50.420 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.009 0.072 20028 Z= 0.605 Angle : 0.846 9.271 27108 Z= 0.543 Chirality : 0.064 0.457 3078 Planarity : 0.005 0.049 3456 Dihedral : 15.879 85.912 7140 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.54 % Allowed : 15.43 % Favored : 83.02 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 8.33 % 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: 0.64 (0.17), residues: 2538 helix: 0.86 (0.13), residues: 1662 sheet: None (None), residues: 0 loop : -0.26 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 240 HIS 0.009 0.001 HIS F 63 PHE 0.022 0.001 PHE D 158 TYR 0.021 0.002 TYR E 305 ARG 0.011 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 582 time to evaluate : 2.030 Fit side-chains REVERT: B 220 PHE cc_start: 0.7959 (t80) cc_final: 0.7728 (t80) REVERT: C 261 ASP cc_start: 0.7070 (m-30) cc_final: 0.6648 (m-30) REVERT: D 261 ASP cc_start: 0.6989 (m-30) cc_final: 0.6678 (m-30) REVERT: E 261 ASP cc_start: 0.7121 (m-30) cc_final: 0.6686 (m-30) outliers start: 30 outliers final: 7 residues processed: 589 average time/residue: 1.4205 time to fit residues: 929.5165 Evaluate side-chains 539 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 532 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 147 optimal weight: 0.4980 chunk 228 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 161 ASN A 361 ASN B 153 GLN B 345 GLN C 393 HIS D 3 ASN D 153 GLN D 343 ASN D 361 ASN E 3 ASN E 161 ASN F 3 ASN F 343 ASN F 347 GLN F 393 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20028 Z= 0.171 Angle : 0.439 4.783 27108 Z= 0.240 Chirality : 0.035 0.151 3078 Planarity : 0.004 0.037 3456 Dihedral : 4.122 54.420 2831 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.34 % Allowed : 17.18 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.72 (0.17), residues: 2538 helix: 1.73 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.15 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 240 HIS 0.005 0.001 HIS A 393 PHE 0.014 0.001 PHE F 220 TYR 0.018 0.001 TYR B 305 ARG 0.007 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 543 time to evaluate : 2.238 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.6841 (m-30) cc_final: 0.6592 (m-30) REVERT: B 373 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7879 (t80) outliers start: 65 outliers final: 22 residues processed: 574 average time/residue: 1.4718 time to fit residues: 937.0070 Evaluate side-chains 564 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 541 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 400 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 343 ASN A 361 ASN A 389 ASN A 395 ASN B 161 ASN B 267 ASN B 389 ASN B 395 ASN C 153 GLN C 389 ASN C 393 HIS C 395 ASN D 3 ASN D 161 ASN D 316 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 214 GLN E 345 GLN E 395 ASN F 170 GLN F 343 ASN F 395 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 20028 Z= 0.469 Angle : 0.572 5.848 27108 Z= 0.306 Chirality : 0.045 0.145 3078 Planarity : 0.005 0.042 3456 Dihedral : 4.098 34.172 2820 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.37 % Allowed : 18.00 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.23 (0.16), residues: 2538 helix: 1.38 (0.12), residues: 1638 sheet: None (None), residues: 0 loop : -0.11 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 240 HIS 0.008 0.002 HIS C 243 PHE 0.024 0.002 PHE C 220 TYR 0.022 0.002 TYR B 305 ARG 0.007 0.001 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 566 time to evaluate : 2.167 Fit side-chains REVERT: C 136 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: D 49 ASP cc_start: 0.7041 (m-30) cc_final: 0.6837 (m-30) REVERT: D 136 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7792 (tttm) outliers start: 46 outliers final: 28 residues processed: 588 average time/residue: 1.4146 time to fit residues: 924.9273 Evaluate side-chains 581 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 551 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 243 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN C 3 ASN C 120 ASN D 3 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 214 GLN F 6 HIS F 120 ASN F 176 GLN F 267 ASN F 343 ASN ** F 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20028 Z= 0.195 Angle : 0.446 6.065 27108 Z= 0.242 Chirality : 0.035 0.134 3078 Planarity : 0.004 0.040 3456 Dihedral : 3.655 22.572 2816 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.93 % Allowed : 18.36 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.56 (0.16), residues: 2538 helix: 1.66 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.04 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 240 HIS 0.004 0.001 HIS E 393 PHE 0.019 0.001 PHE A 220 TYR 0.011 0.001 TYR D 210 ARG 0.008 0.000 ARG D 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 558 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 136 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7686 (tmtm) REVERT: E 150 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7865 (mtpt) REVERT: E 195 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6979 (mt-10) outliers start: 57 outliers final: 36 residues processed: 588 average time/residue: 1.4437 time to fit residues: 943.2489 Evaluate side-chains 582 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 544 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 181 optimal weight: 0.4980 chunk 100 optimal weight: 0.2980 chunk 207 optimal weight: 0.0670 chunk 168 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 176 GLN A 361 ASN B 153 GLN B 161 ASN C 170 GLN D 3 ASN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 120 ASN E 161 ASN F 120 ASN F 176 GLN F 267 ASN F 343 ASN F 353 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20028 Z= 0.191 Angle : 0.441 5.576 27108 Z= 0.238 Chirality : 0.035 0.134 3078 Planarity : 0.004 0.038 3456 Dihedral : 3.558 22.427 2816 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.14 % Allowed : 19.34 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.68 (0.17), residues: 2538 helix: 1.76 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.00 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 240 HIS 0.003 0.001 HIS E 393 PHE 0.017 0.001 PHE C 220 TYR 0.010 0.001 TYR D 210 ARG 0.008 0.000 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 544 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8029 (mp-120) REVERT: C 136 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7703 (tttm) REVERT: D 136 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7696 (tmtm) REVERT: E 150 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7857 (mtpt) REVERT: E 195 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6990 (mt-10) outliers start: 61 outliers final: 39 residues processed: 577 average time/residue: 1.4717 time to fit residues: 941.9698 Evaluate side-chains 594 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 551 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 361 ASN B 153 GLN B 161 ASN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 170 GLN F 3 ASN F 176 GLN F 343 ASN F 353 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20028 Z= 0.275 Angle : 0.482 6.175 27108 Z= 0.258 Chirality : 0.038 0.138 3078 Planarity : 0.004 0.040 3456 Dihedral : 3.699 22.818 2816 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.24 % Allowed : 19.03 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.55 (0.16), residues: 2538 helix: 1.64 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.02 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 240 HIS 0.005 0.001 HIS B 243 PHE 0.020 0.002 PHE F 220 TYR 0.011 0.001 TYR B 305 ARG 0.009 0.001 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 550 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: D 136 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7714 (tmtm) REVERT: D 153 GLN cc_start: 0.8609 (tp40) cc_final: 0.8357 (tp-100) REVERT: D 216 GLU cc_start: 0.6743 (mp0) cc_final: 0.6540 (mp0) REVERT: E 150 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7881 (mtpt) REVERT: E 176 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7397 (mp10) outliers start: 63 outliers final: 41 residues processed: 582 average time/residue: 1.4645 time to fit residues: 945.3348 Evaluate side-chains 599 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 554 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 242 optimal weight: 0.0030 chunk 152 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 361 ASN B 153 GLN B 161 ASN C 170 GLN C 361 ASN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 170 GLN F 3 ASN F 343 ASN F 353 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20028 Z= 0.248 Angle : 0.475 7.325 27108 Z= 0.254 Chirality : 0.037 0.134 3078 Planarity : 0.004 0.040 3456 Dihedral : 3.670 22.170 2816 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.09 % Allowed : 19.29 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.89 (0.17), residues: 2538 helix: 1.81 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : 0.42 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 240 HIS 0.004 0.001 HIS B 243 PHE 0.020 0.001 PHE F 220 TYR 0.011 0.001 TYR C 293 ARG 0.009 0.001 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 542 time to evaluate : 2.423 Fit side-chains revert: symmetry clash REVERT: A 439 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7402 (mmtt) REVERT: B 216 GLU cc_start: 0.6840 (mp0) cc_final: 0.6604 (mp0) REVERT: C 136 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7705 (tttm) REVERT: D 136 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7731 (tmtm) REVERT: D 216 GLU cc_start: 0.6730 (mp0) cc_final: 0.6530 (mp0) REVERT: E 150 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7872 (mtpt) outliers start: 60 outliers final: 40 residues processed: 573 average time/residue: 1.4832 time to fit residues: 942.3391 Evaluate side-chains 599 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 556 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN B 153 GLN B 161 ASN C 361 ASN D 153 GLN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 170 GLN E 176 GLN F 3 ASN F 343 ASN F 353 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20028 Z= 0.230 Angle : 0.469 6.126 27108 Z= 0.252 Chirality : 0.036 0.135 3078 Planarity : 0.004 0.041 3456 Dihedral : 3.618 21.872 2815 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.88 % Allowed : 19.96 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.85 (0.17), residues: 2538 helix: 1.74 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.40 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 240 HIS 0.004 0.001 HIS B 243 PHE 0.019 0.001 PHE F 220 TYR 0.011 0.001 TYR C 293 ARG 0.009 0.000 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 546 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7411 (mmtt) REVERT: B 216 GLU cc_start: 0.6821 (mp0) cc_final: 0.6609 (mp0) REVERT: C 136 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7705 (tttm) REVERT: D 136 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7725 (tmtm) REVERT: D 216 GLU cc_start: 0.6724 (mp0) cc_final: 0.6523 (mp0) REVERT: E 150 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7867 (mtpt) outliers start: 56 outliers final: 43 residues processed: 573 average time/residue: 1.4843 time to fit residues: 942.8271 Evaluate side-chains 600 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 554 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 0.0370 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 361 ASN B 153 GLN C 361 ASN D 153 GLN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 170 GLN E 176 GLN F 353 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20028 Z= 0.214 Angle : 0.467 6.371 27108 Z= 0.250 Chirality : 0.036 0.147 3078 Planarity : 0.004 0.041 3456 Dihedral : 3.550 20.639 2814 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.30 % Favored : 98.66 % Rotamer: Outliers : 3.09 % Allowed : 19.65 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.89 (0.17), residues: 2538 helix: 1.77 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.43 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 240 HIS 0.004 0.001 HIS C 204 PHE 0.019 0.001 PHE F 220 TYR 0.010 0.001 TYR C 293 ARG 0.009 0.000 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 549 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7453 (mmtt) REVERT: B 216 GLU cc_start: 0.6819 (mp0) cc_final: 0.6606 (mp0) REVERT: C 136 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7701 (tttm) REVERT: E 150 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7867 (mtpt) REVERT: E 176 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7477 (mp-120) outliers start: 60 outliers final: 42 residues processed: 577 average time/residue: 1.4834 time to fit residues: 950.0866 Evaluate side-chains 600 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 555 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 4.9990 chunk 146 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 361 ASN C 361 ASN D 153 GLN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 170 GLN E 176 GLN ** F 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20028 Z= 0.340 Angle : 0.527 6.863 27108 Z= 0.282 Chirality : 0.040 0.146 3078 Planarity : 0.004 0.044 3456 Dihedral : 3.768 19.972 2814 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.65 % Favored : 98.27 % Rotamer: Outliers : 2.57 % Allowed : 20.58 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.34 (0.16), residues: 2538 helix: 1.45 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -0.10 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 4 HIS 0.006 0.001 HIS C 243 PHE 0.023 0.002 PHE F 220 TYR 0.018 0.002 TYR F 210 ARG 0.010 0.001 ARG F 433 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 559 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7467 (mmtt) REVERT: B 216 GLU cc_start: 0.6822 (mp0) cc_final: 0.6605 (mp0) REVERT: C 136 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7749 (tttm) REVERT: E 150 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7907 (mtpt) outliers start: 50 outliers final: 43 residues processed: 583 average time/residue: 1.5048 time to fit residues: 972.2922 Evaluate side-chains 610 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 565 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 200 optimal weight: 0.0050 chunk 83 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 361 ASN B 361 ASN C 361 ASN D 153 GLN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 170 GLN E 176 GLN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 ASN F 347 GLN ** F 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.115262 restraints weight = 22143.107| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.13 r_work: 0.3490 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20028 Z= 0.296 Angle : 0.508 7.724 27108 Z= 0.272 Chirality : 0.039 0.151 3078 Planarity : 0.004 0.041 3456 Dihedral : 3.735 19.382 2814 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.34 % Favored : 98.58 % Rotamer: Outliers : 2.52 % Allowed : 20.88 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.76 (0.17), residues: 2538 helix: 1.70 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : 0.36 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 240 HIS 0.005 0.001 HIS C 243 PHE 0.021 0.002 PHE F 220 TYR 0.015 0.001 TYR F 210 ARG 0.009 0.001 ARG D 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12194.92 seconds wall clock time: 213 minutes 14.68 seconds (12794.68 seconds total)