Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 01:44:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/05_2023/7tu5_26126.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/05_2023/7tu5_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_26126/05_2023/7tu5_26126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/05_2023/7tu5_26126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/05_2023/7tu5_26126.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tu5_26126/05_2023/7tu5_26126.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 10.13, per 1000 atoms: 0.52 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: 7.90 Conformation dependent library (CDL) restraints added in 2.9 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: 0.92 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: 5.63 Time building geometry restraints manager: 8.46 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.020 Extract box with map and model: 11.710 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 48.350 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.930 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.204 Fit side-chains outliers start: 30 outliers final: 7 residues processed: 589 average time/residue: 1.4626 time to fit residues: 956.5402 Evaluate side-chains 540 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 533 time to evaluate : 2.398 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 1.2592 time to fit residues: 8.9533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 20028 Z= 0.173 Angle : 0.440 4.770 27108 Z= 0.241 Chirality : 0.035 0.147 3078 Planarity : 0.004 0.037 3456 Dihedral : 3.400 18.755 2814 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 3.24 % 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: 1.74 (0.17), residues: 2538 helix: 1.74 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.16 (0.22), residues: 900 *********************** 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 603 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 540 time to evaluate : 2.358 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 22 residues processed: 571 average time/residue: 1.5149 time to fit residues: 958.2078 Evaluate side-chains 555 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 533 time to evaluate : 2.298 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 8 residues processed: 14 average time/residue: 0.8680 time to fit residues: 17.2076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 190 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 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: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 267 ASN B 395 ASN C 153 GLN C 345 GLN C 389 ASN C 393 HIS C 395 ASN D 3 ASN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 214 GLN E 395 ASN F 170 GLN F 343 ASN F 395 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 20028 Z= 0.363 Angle : 0.527 5.062 27108 Z= 0.282 Chirality : 0.041 0.139 3078 Planarity : 0.004 0.041 3456 Dihedral : 3.787 19.329 2814 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 2.67 % 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: 1.40 (0.16), residues: 2538 helix: 1.53 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.07 (0.20), residues: 900 *********************** 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 608 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 556 time to evaluate : 2.368 Fit side-chains outliers start: 52 outliers final: 27 residues processed: 578 average time/residue: 1.4827 time to fit residues: 951.7970 Evaluate side-chains 569 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 542 time to evaluate : 2.219 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 10 residues processed: 17 average time/residue: 0.8612 time to fit residues: 20.4617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.3980 chunk 172 optimal weight: 0.0050 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 161 ASN C 3 ASN C 361 ASN C 393 HIS D 3 ASN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 214 GLN E 361 ASN F 6 HIS F 120 ASN F 267 ASN F 343 ASN ** F 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 20028 Z= 0.164 Angle : 0.424 4.984 27108 Z= 0.231 Chirality : 0.034 0.131 3078 Planarity : 0.003 0.038 3456 Dihedral : 3.459 17.972 2814 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 2.67 % 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: 1.70 (0.17), residues: 2538 helix: 1.79 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.02 (0.21), residues: 900 *********************** 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 590 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 538 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 34 residues processed: 569 average time/residue: 1.5349 time to fit residues: 968.7036 Evaluate side-chains 563 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 529 time to evaluate : 2.256 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 21 residues processed: 13 average time/residue: 0.9592 time to fit residues: 17.6842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 181 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 168 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 A 389 ASN B 153 GLN B 161 ASN C 3 ASN C 161 ASN C 170 GLN C 393 HIS D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 120 ASN E 161 ASN E 361 ASN F 3 ASN F 353 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 20028 Z= 0.186 Angle : 0.441 6.662 27108 Z= 0.236 Chirality : 0.035 0.138 3078 Planarity : 0.003 0.037 3456 Dihedral : 3.432 19.400 2814 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 3.14 % 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: 1.75 (0.17), residues: 2538 helix: 1.83 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.01 (0.21), residues: 900 *********************** 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 596 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 535 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 41 residues processed: 567 average time/residue: 1.5135 time to fit residues: 952.3179 Evaluate side-chains 581 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 540 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 23 residues processed: 18 average time/residue: 0.8193 time to fit residues: 20.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 60 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 161 ASN C 393 HIS D 153 GLN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 170 GLN E 361 ASN F 3 ASN F 343 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 20028 Z= 0.294 Angle : 0.490 5.991 27108 Z= 0.262 Chirality : 0.038 0.145 3078 Planarity : 0.004 0.039 3456 Dihedral : 3.657 20.967 2814 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 2.93 % 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: 1.66 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.05 (0.20), residues: 900 *********************** 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 595 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 538 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 39 residues processed: 569 average time/residue: 1.5520 time to fit residues: 983.0890 Evaluate side-chains 573 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 534 time to evaluate : 2.279 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 22 residues processed: 17 average time/residue: 0.6897 time to fit residues: 17.5952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 242 optimal weight: 0.0670 chunk 152 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN B 153 GLN B 161 ASN C 120 ASN C 393 HIS D 153 GLN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 170 GLN E 176 GLN E 361 ASN F 3 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2362 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= 0.216 Angle : 0.461 6.307 27108 Z= 0.247 Chirality : 0.036 0.146 3078 Planarity : 0.004 0.039 3456 Dihedral : 3.561 21.287 2814 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 2.67 % 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: 1.99 (0.17), residues: 2538 helix: 1.89 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : 0.44 (0.22), residues: 936 *********************** 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 582 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 530 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 36 residues processed: 560 average time/residue: 1.5410 time to fit residues: 958.8907 Evaluate side-chains 567 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 531 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 23 residues processed: 13 average time/residue: 0.9736 time to fit residues: 18.2381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 165 optimal weight: 0.0000 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 220 optimal weight: 0.7980 overall best weight: 0.8788 ------------------------------------------------------------------------------- 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 A 389 ASN C 161 ASN C 393 HIS D 153 GLN D 161 ASN D 343 ASN D 361 ASN E 3 ASN E 161 ASN E 170 GLN E 361 ASN F 3 ASN F 343 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2378 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= 0.207 Angle : 0.461 8.139 27108 Z= 0.246 Chirality : 0.036 0.154 3078 Planarity : 0.004 0.040 3456 Dihedral : 3.520 20.785 2814 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 2.37 % 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: 1.62 (0.17), residues: 2538 helix: 1.68 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -0.04 (0.21), residues: 864 *********************** 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 576 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 530 time to evaluate : 2.342 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 37 residues processed: 557 average time/residue: 1.4360 time to fit residues: 887.5057 Evaluate side-chains 568 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 531 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 23 residues processed: 14 average time/residue: 0.6312 time to fit residues: 12.8599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 204 optimal weight: 0.6980 chunk 214 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: