Starting phenix.real_space_refine on Fri Mar 15 06:44:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/03_2024/7ao8_11837_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/03_2024/7ao8_11837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/03_2024/7ao8_11837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/03_2024/7ao8_11837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/03_2024/7ao8_11837_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/03_2024/7ao8_11837_neut_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 2 6.06 5 P 12 5.49 5 S 59 5.16 5 C 6897 2.51 5 N 1837 2.21 5 O 2094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ASP 176": "OD1" <-> "OD2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 321": "OD1" <-> "OD2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 321": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10905 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 487 Classifications: {'peptide': 64} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2206 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 266} Chain breaks: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2206 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 266} Chain breaks: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2964 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2964 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 IHP D 801 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP D 801 " occ=0.70 residue: pdb=" C1 IHP A 801 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP A 801 " occ=0.70 Time building chain proxies: 5.78, per 1000 atoms: 0.53 Number of scatterers: 10905 At special positions: 0 Unit cell: (206.01, 85.02, 92.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 K 4 19.00 S 59 16.00 P 12 15.00 O 2094 8.00 N 1837 7.00 C 6897 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: 3.99 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 178 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 178 " 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 9 sheets defined 38.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'C' and resid 190 through 200 removed outlier: 6.690A pdb=" N ASN C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR C 200 " --> pdb=" O TYR C 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 207 through 227 Processing helix chain 'D' and resid 238 through 245 Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 265 through 273 removed outlier: 3.791A pdb=" N SER D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 287 No H-bonds generated for 'chain 'D' and resid 284 through 287' Processing helix chain 'D' and resid 290 through 303 removed outlier: 3.620A pdb=" N GLU D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 313 Processing helix chain 'D' and resid 320 through 332 removed outlier: 4.020A pdb=" N THR D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 207 through 227 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 265 through 273 removed outlier: 3.792A pdb=" N SER A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.620A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 320 through 332 removed outlier: 4.021A pdb=" N THR A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 20 removed outlier: 3.847A pdb=" N GLY E 20 " --> pdb=" O GLY E 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 20' Processing helix chain 'E' and resid 32 through 44 removed outlier: 3.508A pdb=" N HIS E 39 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN E 40 " --> pdb=" O MET E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 61 through 64 No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 84 through 94 removed outlier: 3.595A pdb=" N SER E 88 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN E 90 " --> pdb=" O GLU E 86 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 155 through 165 removed outlier: 3.909A pdb=" N LYS E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 187 removed outlier: 3.556A pdb=" N PHE E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 234 through 252 Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 278 through 291 removed outlier: 3.646A pdb=" N CYS E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 319 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 356 through 372 removed outlier: 3.527A pdb=" N ILE E 362 " --> pdb=" O TYR E 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 20 removed outlier: 3.848A pdb=" N GLY B 20 " --> pdb=" O GLY B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 20' Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.509A pdb=" N HIS B 39 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 40 " --> pdb=" O MET B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 61 through 64 No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 84 through 94 removed outlier: 3.594A pdb=" N SER B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 125 Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.909A pdb=" N LYS B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.556A pdb=" N PHE B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 234 through 252 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.646A pdb=" N CYS B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 285 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 319 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 356 through 372 removed outlier: 3.527A pdb=" N ILE B 362 " --> pdb=" O TYR B 358 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 160 through 165 Processing sheet with id= B, first strand: chain 'D' and resid 122 through 126 removed outlier: 6.655A pdb=" N TYR D 13 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS D 125 " --> pdb=" O TYR D 11 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TYR D 11 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 23 " --> pdb=" O PHE D 14 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE D 24 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS D 41 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU D 30 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU D 39 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 45 through 47 removed outlier: 6.858A pdb=" N LEU D 151 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 127 through 130 Processing sheet with id= E, first strand: chain 'A' and resid 122 through 126 removed outlier: 6.656A pdb=" N TYR A 13 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS A 125 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR A 11 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 23 " --> pdb=" O PHE A 14 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 24 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 41 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU A 30 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU A 39 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.858A pdb=" N LEU A 151 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 127 through 130 Processing sheet with id= H, first strand: chain 'E' and resid 52 through 54 removed outlier: 6.918A pdb=" N ILE E 131 " --> pdb=" O CYS E 12 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TYR E 14 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL E 133 " --> pdb=" O TYR E 14 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET E 295 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASN E 134 " --> pdb=" O MET E 295 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET E 297 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL E 257 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU E 298 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 259 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 52 through 54 removed outlier: 6.919A pdb=" N ILE B 131 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N TYR B 14 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 133 " --> pdb=" O TYR B 14 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET B 295 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASN B 134 " --> pdb=" O MET B 295 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET B 297 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 257 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU B 298 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 259 " --> pdb=" O LEU B 298 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1815 1.31 - 1.44: 3183 1.44 - 1.57: 6036 1.57 - 1.70: 23 1.70 - 1.83: 95 Bond restraints: 11152 Sorted by residual: bond pdb=" CA ILE A 51 " pdb=" C ILE A 51 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.27e-02 6.20e+03 2.74e+01 bond pdb=" CA ILE D 51 " pdb=" C ILE D 51 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.27e-02 6.20e+03 2.71e+01 bond pdb=" CA ILE D 51 " pdb=" CB ILE D 51 " ideal model delta sigma weight residual 1.540 1.472 0.068 1.36e-02 5.41e+03 2.47e+01 bond pdb=" CA ILE A 51 " pdb=" CB ILE A 51 " ideal model delta sigma weight residual 1.540 1.473 0.067 1.36e-02 5.41e+03 2.44e+01 bond pdb=" C GLY E 299 " pdb=" O GLY E 299 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.35e-02 5.49e+03 1.79e+01 ... (remaining 11147 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.87: 285 105.87 - 112.95: 5267 112.95 - 120.03: 4314 120.03 - 127.12: 5116 127.12 - 134.20: 114 Bond angle restraints: 15096 Sorted by residual: angle pdb=" CA ASN A 31 " pdb=" CB ASN A 31 " pdb=" CG ASN A 31 " ideal model delta sigma weight residual 112.60 105.88 6.72 1.00e+00 1.00e+00 4.52e+01 angle pdb=" CA ASN D 31 " pdb=" CB ASN D 31 " pdb=" CG ASN D 31 " ideal model delta sigma weight residual 112.60 105.91 6.69 1.00e+00 1.00e+00 4.47e+01 angle pdb=" C ARG D 143 " pdb=" N GLU D 144 " pdb=" CA GLU D 144 " ideal model delta sigma weight residual 120.28 129.61 -9.33 1.44e+00 4.82e-01 4.20e+01 angle pdb=" C ARG A 143 " pdb=" N GLU A 144 " pdb=" CA GLU A 144 " ideal model delta sigma weight residual 120.28 129.46 -9.18 1.44e+00 4.82e-01 4.07e+01 angle pdb=" C GLY D 36 " pdb=" N ASN D 37 " pdb=" CA ASN D 37 " ideal model delta sigma weight residual 120.71 129.68 -8.97 1.42e+00 4.96e-01 3.99e+01 ... (remaining 15091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 6195 24.14 - 48.28: 372 48.28 - 72.42: 59 72.42 - 96.56: 26 96.56 - 120.70: 12 Dihedral angle restraints: 6664 sinusoidal: 2718 harmonic: 3946 Sorted by residual: dihedral pdb=" C SER D 52 " pdb=" N SER D 52 " pdb=" CA SER D 52 " pdb=" CB SER D 52 " ideal model delta harmonic sigma weight residual -122.60 -138.48 15.88 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" C SER A 52 " pdb=" N SER A 52 " pdb=" CA SER A 52 " pdb=" CB SER A 52 " ideal model delta harmonic sigma weight residual -122.60 -138.42 15.82 0 2.50e+00 1.60e-01 4.01e+01 dihedral pdb=" C HIS A 101 " pdb=" N HIS A 101 " pdb=" CA HIS A 101 " pdb=" CB HIS A 101 " ideal model delta harmonic sigma weight residual -122.60 -135.95 13.35 0 2.50e+00 1.60e-01 2.85e+01 ... (remaining 6661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 1592 1.007 - 2.013: 0 2.013 - 3.020: 0 3.020 - 4.027: 0 4.027 - 5.034: 4 Chirality restraints: 1596 Sorted by residual: chirality pdb=" C2 IHP D 801 " pdb=" C1 IHP D 801 " pdb=" C3 IHP D 801 " pdb=" O12 IHP D 801 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C2 IHP A 801 " pdb=" C1 IHP A 801 " pdb=" C3 IHP A 801 " pdb=" O12 IHP A 801 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C3 IHP D 801 " pdb=" C2 IHP D 801 " pdb=" C4 IHP D 801 " pdb=" O13 IHP D 801 " both_signs ideal model delta sigma weight residual False -2.34 2.39 -4.73 2.00e-01 2.50e+01 5.60e+02 ... (remaining 1593 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 109 " 0.271 2.00e-02 2.50e+03 1.86e-01 6.05e+02 pdb=" CG PHE D 109 " -0.115 2.00e-02 2.50e+03 pdb=" CD1 PHE D 109 " -0.147 2.00e-02 2.50e+03 pdb=" CD2 PHE D 109 " -0.260 2.00e-02 2.50e+03 pdb=" CE1 PHE D 109 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 PHE D 109 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE D 109 " 0.249 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 109 " -0.271 2.00e-02 2.50e+03 1.86e-01 6.04e+02 pdb=" CG PHE A 109 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE A 109 " 0.147 2.00e-02 2.50e+03 pdb=" CD2 PHE A 109 " 0.260 2.00e-02 2.50e+03 pdb=" CE1 PHE A 109 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 PHE A 109 " -0.047 2.00e-02 2.50e+03 pdb=" CZ PHE A 109 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 153 " -0.085 2.00e-02 2.50e+03 5.85e-02 6.85e+01 pdb=" CG TYR A 153 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 153 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 153 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 153 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR A 153 " 0.047 2.00e-02 2.50e+03 pdb=" CZ TYR A 153 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR A 153 " -0.110 2.00e-02 2.50e+03 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 1.22 - 2.00: 13 2.00 - 2.79: 2222 2.79 - 3.57: 17818 3.57 - 4.36: 34347 4.36 - 5.14: 56765 Nonbonded interactions: 111165 Sorted by model distance: nonbonded pdb=" OD1 ASP D 163 " pdb=" OE1 GLN E 353 " model vdw 1.219 3.040 nonbonded pdb=" CB PRO C 153 " pdb=" SD MET B 84 " model vdw 1.235 3.800 nonbonded pdb=" CG ASP D 163 " pdb=" OE1 GLN E 353 " model vdw 1.299 3.270 nonbonded pdb=" OE1 GLU D 135 " pdb=" NZ LYS E 361 " model vdw 1.611 2.520 nonbonded pdb=" CG1 ILE C 165 " pdb=" O GLU A 301 " model vdw 1.766 3.440 ... (remaining 111160 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.950 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.110 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.068 11152 Z= 0.705 Angle : 1.515 10.400 15096 Z= 0.983 Chirality : 0.259 5.034 1596 Planarity : 0.011 0.186 1946 Dihedral : 17.193 120.702 4142 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.87 % Favored : 92.52 % Rotamer: Outliers : 4.18 % Allowed : 7.06 % Favored : 88.76 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.19), residues: 1324 helix: -2.91 (0.16), residues: 544 sheet: -1.04 (0.36), residues: 180 loop : -1.95 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 159 HIS 0.009 0.002 HIS D 121 PHE 0.271 0.012 PHE A 109 TYR 0.110 0.008 TYR D 153 ARG 0.031 0.003 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 144 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 VAL cc_start: 0.3628 (OUTLIER) cc_final: 0.3321 (m) REVERT: A 269 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6423 (tp) REVERT: E 47 LEU cc_start: 0.8178 (mt) cc_final: 0.7760 (mm) REVERT: E 82 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: B 45 TYR cc_start: 0.6913 (m-80) cc_final: 0.6487 (m-80) REVERT: B 82 ASP cc_start: 0.4851 (OUTLIER) cc_final: 0.4416 (m-30) REVERT: B 313 THR cc_start: 0.7810 (m) cc_final: 0.7439 (m) outliers start: 48 outliers final: 2 residues processed: 187 average time/residue: 0.2557 time to fit residues: 65.2983 Evaluate side-chains 88 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 191 GLN D 197 GLN D 261 ASN A 203 ASN A 253 HIS A 261 ASN E 26 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN E 141 HIS ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 375 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4536 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 11152 Z= 0.383 Angle : 0.947 13.419 15096 Z= 0.487 Chirality : 0.051 0.276 1596 Planarity : 0.007 0.082 1946 Dihedral : 7.330 57.644 1580 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.44 % Allowed : 5.31 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.93 (0.21), residues: 1324 helix: -1.32 (0.20), residues: 532 sheet: -0.74 (0.37), residues: 172 loop : -1.26 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 312 HIS 0.019 0.003 HIS B 199 PHE 0.032 0.003 PHE E 198 TYR 0.033 0.003 TYR E 72 ARG 0.007 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 MET cc_start: 0.2818 (ttt) cc_final: 0.2399 (mtp) REVERT: E 249 MET cc_start: 0.6756 (tpt) cc_final: 0.6258 (tpt) REVERT: B 226 TYR cc_start: 0.5387 (t80) cc_final: 0.5115 (t80) outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 0.2408 time to fit residues: 35.4721 Evaluate side-chains 73 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.0170 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 overall best weight: 3.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 ASN A 132 ASN A 197 GLN A 261 ASN A 312 GLN E 26 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 HIS B 33 HIS ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 353 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4722 moved from start: 0.7943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11152 Z= 0.265 Angle : 0.693 7.726 15096 Z= 0.366 Chirality : 0.044 0.307 1596 Planarity : 0.005 0.062 1946 Dihedral : 6.803 56.273 1580 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.22 (0.22), residues: 1324 helix: -0.37 (0.22), residues: 527 sheet: -0.62 (0.38), residues: 175 loop : -1.16 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 288 HIS 0.015 0.002 HIS E 199 PHE 0.018 0.002 PHE A 223 TYR 0.023 0.002 TYR E 303 ARG 0.005 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 MET cc_start: 0.3409 (ttt) cc_final: 0.2348 (mtm) REVERT: E 249 MET cc_start: 0.6571 (tpt) cc_final: 0.6218 (tpt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2273 time to fit residues: 26.7178 Evaluate side-chains 61 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN D 174 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5236 moved from start: 1.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 11152 Z= 0.467 Angle : 0.962 14.419 15096 Z= 0.517 Chirality : 0.051 0.303 1596 Planarity : 0.007 0.066 1946 Dihedral : 8.150 45.797 1580 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 39.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.52 % Allowed : 6.36 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.21), residues: 1324 helix: -1.61 (0.20), residues: 514 sheet: -0.39 (0.44), residues: 135 loop : -1.70 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP D 317 HIS 0.014 0.003 HIS D 253 PHE 0.027 0.004 PHE E 337 TYR 0.032 0.004 TYR E 72 ARG 0.010 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.7708 (pmm) cc_final: 0.7494 (pmm) REVERT: B 171 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5721 (tt) outliers start: 6 outliers final: 2 residues processed: 68 average time/residue: 0.2053 time to fit residues: 21.5168 Evaluate side-chains 56 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 132 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 HIS ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5090 moved from start: 1.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11152 Z= 0.262 Angle : 0.695 9.121 15096 Z= 0.367 Chirality : 0.044 0.245 1596 Planarity : 0.005 0.053 1946 Dihedral : 7.291 49.418 1580 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.22), residues: 1324 helix: -0.84 (0.21), residues: 530 sheet: -0.35 (0.47), residues: 131 loop : -1.56 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 330 HIS 0.007 0.002 HIS B 199 PHE 0.015 0.002 PHE D 314 TYR 0.022 0.002 TYR E 72 ARG 0.004 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.198 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1832 time to fit residues: 18.6499 Evaluate side-chains 51 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5112 moved from start: 1.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11152 Z= 0.241 Angle : 0.658 8.892 15096 Z= 0.346 Chirality : 0.042 0.198 1596 Planarity : 0.004 0.043 1946 Dihedral : 7.114 53.994 1580 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.54 (0.22), residues: 1324 helix: -0.43 (0.22), residues: 525 sheet: -0.32 (0.46), residues: 129 loop : -1.64 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 199 HIS 0.006 0.001 HIS B 57 PHE 0.012 0.002 PHE B 75 TYR 0.021 0.002 TYR E 72 ARG 0.005 0.001 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.361 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1872 time to fit residues: 18.7318 Evaluate side-chains 51 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 79 optimal weight: 0.0070 chunk 77 optimal weight: 20.0000 chunk 58 optimal weight: 0.0070 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 132 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4937 moved from start: 1.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11152 Z= 0.153 Angle : 0.564 7.803 15096 Z= 0.291 Chirality : 0.041 0.218 1596 Planarity : 0.004 0.043 1946 Dihedral : 6.491 56.537 1580 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.88 (0.23), residues: 1324 helix: 0.36 (0.24), residues: 517 sheet: -0.46 (0.43), residues: 145 loop : -1.37 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 317 HIS 0.004 0.001 HIS B 57 PHE 0.015 0.001 PHE D 213 TYR 0.018 0.001 TYR A 46 ARG 0.004 0.000 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: E 289 LYS cc_start: 0.6869 (tttt) cc_final: 0.6494 (tppt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1963 time to fit residues: 20.7325 Evaluate side-chains 51 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5131 moved from start: 1.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11152 Z= 0.236 Angle : 0.639 7.701 15096 Z= 0.336 Chirality : 0.042 0.150 1596 Planarity : 0.004 0.043 1946 Dihedral : 6.792 57.846 1580 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.19 (0.23), residues: 1324 helix: 0.03 (0.23), residues: 525 sheet: -0.44 (0.45), residues: 129 loop : -1.53 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 317 HIS 0.006 0.002 HIS B 57 PHE 0.024 0.002 PHE B 241 TYR 0.036 0.002 TYR E 22 ARG 0.003 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.148 Fit side-chains REVERT: E 289 LYS cc_start: 0.7017 (tttt) cc_final: 0.6561 (tppt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1973 time to fit residues: 19.1021 Evaluate side-chains 51 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 71 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 moved from start: 1.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11152 Z= 0.278 Angle : 0.708 9.580 15096 Z= 0.374 Chirality : 0.044 0.202 1596 Planarity : 0.005 0.052 1946 Dihedral : 7.020 58.988 1580 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 28.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.48 (0.22), residues: 1324 helix: -0.33 (0.22), residues: 527 sheet: -0.75 (0.43), residues: 134 loop : -1.54 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 199 HIS 0.011 0.002 HIS A 253 PHE 0.021 0.002 PHE A 109 TYR 0.026 0.002 TYR B 221 ARG 0.008 0.001 ARG E 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.426 Fit side-chains REVERT: E 84 MET cc_start: 0.3202 (mtt) cc_final: 0.2984 (mtt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1960 time to fit residues: 18.6428 Evaluate side-chains 48 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 32 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 191 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5046 moved from start: 1.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11152 Z= 0.163 Angle : 0.579 9.866 15096 Z= 0.300 Chirality : 0.041 0.202 1596 Planarity : 0.004 0.048 1946 Dihedral : 6.478 58.590 1580 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.96 (0.23), residues: 1324 helix: 0.26 (0.23), residues: 525 sheet: -0.52 (0.44), residues: 134 loop : -1.40 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 199 HIS 0.005 0.001 HIS B 199 PHE 0.020 0.001 PHE B 241 TYR 0.023 0.001 TYR E 221 ARG 0.008 0.000 ARG E 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.321 Fit side-chains REVERT: E 84 MET cc_start: 0.3131 (mtt) cc_final: 0.2869 (mtt) REVERT: E 295 MET cc_start: 0.6679 (mtt) cc_final: 0.6361 (mmt) REVERT: E 350 MET cc_start: 0.1667 (ppp) cc_final: 0.1433 (ppp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1861 time to fit residues: 18.6509 Evaluate side-chains 52 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 0.0770 chunk 107 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.051971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.036939 restraints weight = 117160.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.037800 restraints weight = 87578.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.038516 restraints weight = 71814.307| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 1.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11152 Z= 0.277 Angle : 0.693 10.199 15096 Z= 0.367 Chirality : 0.043 0.195 1596 Planarity : 0.005 0.049 1946 Dihedral : 6.904 56.306 1580 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 29.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.23), residues: 1324 helix: -0.22 (0.22), residues: 520 sheet: -0.83 (0.44), residues: 136 loop : -1.51 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 199 HIS 0.008 0.002 HIS B 199 PHE 0.020 0.002 PHE B 241 TYR 0.024 0.002 TYR B 221 ARG 0.006 0.001 ARG E 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.43 seconds wall clock time: 35 minutes 13.68 seconds (2113.68 seconds total)