Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 02:31:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/08_2023/7ao8_11837_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/08_2023/7ao8_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_11837/08_2023/7ao8_11837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/08_2023/7ao8_11837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/08_2023/7ao8_11837_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ao8_11837/08_2023/7ao8_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 5.72, per 1000 atoms: 0.52 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: 4.45 Conformation dependent library (CDL) restraints added in 1.6 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: 1.79 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: 2.96 Time building geometry restraints manager: 4.77 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 - 17.66: 5893 17.66 - 35.32: 492 35.32 - 52.99: 143 52.99 - 70.65: 36 70.65 - 88.31: 28 Dihedral angle restraints: 6592 sinusoidal: 2646 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 6589 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: 1.110 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: 6.340 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.230 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.240 ------------------------------------------------------------------------------- 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 : 16.210 88.309 4070 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 % 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 *********************** 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 : 1.402 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 outliers start: 48 outliers final: 2 residues processed: 187 average time/residue: 0.2660 time to fit residues: 67.9708 Evaluate side-chains 83 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3568 time to fit residues: 2.6011 ------------------------------------------------------------------------------- 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: 0.7980 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: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 GLN D 261 ASN A 197 GLN A 253 HIS A 261 ASN E 26 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN E 57 HIS 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 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4249 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 11152 Z= 0.305 Angle : 0.824 11.417 15096 Z= 0.418 Chirality : 0.047 0.467 1596 Planarity : 0.005 0.041 1946 Dihedral : 5.642 28.850 1508 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.26 % 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: -1.53 (0.21), residues: 1324 helix: -0.78 (0.21), residues: 543 sheet: -0.74 (0.37), residues: 175 loop : -1.20 (0.22), residues: 606 *********************** 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 101 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 0.2433 time to fit residues: 35.6621 Evaluate side-chains 76 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1027 time to fit residues: 1.9026 ------------------------------------------------------------------------------- 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: 0.9980 chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 A 20 ASN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN A 261 ASN A 312 GLN E 26 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** E 354 ASN ** 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 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS B 353 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4733 moved from start: 0.7839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 11152 Z= 0.299 Angle : 0.746 9.333 15096 Z= 0.399 Chirality : 0.045 0.341 1596 Planarity : 0.005 0.045 1946 Dihedral : 5.715 33.913 1508 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 24.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.09 % 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: -1.20 (0.22), residues: 1324 helix: -0.43 (0.22), residues: 528 sheet: -0.65 (0.38), residues: 175 loop : -1.06 (0.24), residues: 621 *********************** 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 84 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.329 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 outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.2631 time to fit residues: 31.9853 Evaluate side-chains 64 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0988 time to fit residues: 1.8884 ------------------------------------------------------------------------------- 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: 5.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 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** A 20 ASN A 102 GLN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 HIS ** 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 39 HIS ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 moved from start: 1.1405 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 : 0.992 14.637 15096 Z= 0.531 Chirality : 0.052 0.318 1596 Planarity : 0.007 0.065 1946 Dihedral : 7.561 47.733 1508 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 41.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.45 % Rotamer Outliers : 0.70 % 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: -2.64 (0.20), residues: 1324 helix: -1.80 (0.19), residues: 518 sheet: -0.75 (0.43), residues: 140 loop : -1.88 (0.21), residues: 666 *********************** 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 73 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 73 average time/residue: 0.2189 time to fit residues: 24.4764 Evaluate side-chains 57 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1371 time to fit residues: 1.9989 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** A 20 ASN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN A 253 HIS ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 HIS ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS B 44 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5119 moved from start: 1.1662 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= 0.276 Angle : 0.716 9.149 15096 Z= 0.380 Chirality : 0.044 0.248 1596 Planarity : 0.005 0.044 1946 Dihedral : 6.601 47.837 1508 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 27.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.00 % 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: -2.07 (0.21), residues: 1324 helix: -1.15 (0.20), residues: 530 sheet: -0.38 (0.47), residues: 131 loop : -1.73 (0.22), residues: 663 *********************** 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 66 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2125 time to fit residues: 21.9701 Evaluate side-chains 56 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5997 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN B 33 HIS ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 moved from start: 1.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 11152 Z= 0.227 Angle : 0.645 9.322 15096 Z= 0.338 Chirality : 0.042 0.224 1596 Planarity : 0.004 0.044 1946 Dihedral : 6.252 57.747 1508 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 0.00 % 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: -1.64 (0.22), residues: 1324 helix: -0.47 (0.22), residues: 519 sheet: -0.50 (0.46), residues: 133 loop : -1.71 (0.22), residues: 672 *********************** 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 62 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2094 time to fit residues: 21.0405 Evaluate side-chains 53 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6983 ------------------------------------------------------------------------------- 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: 5.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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** A 20 ASN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5189 moved from start: 1.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 11152 Z= 0.266 Angle : 0.693 9.209 15096 Z= 0.365 Chirality : 0.044 0.226 1596 Planarity : 0.005 0.043 1946 Dihedral : 6.461 58.884 1508 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.00 % 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: -1.94 (0.22), residues: 1324 helix: -0.76 (0.22), residues: 535 sheet: -0.73 (0.45), residues: 133 loop : -1.84 (0.23), residues: 656 *********************** 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 57 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.252 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2094 time to fit residues: 19.0024 Evaluate side-chains 49 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5763 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 30.0000 chunk 100 optimal weight: 0.0770 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- 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 294 ASN A 20 ASN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5243 moved from start: 1.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 11152 Z= 0.283 Angle : 0.711 9.178 15096 Z= 0.377 Chirality : 0.044 0.223 1596 Planarity : 0.005 0.045 1946 Dihedral : 6.699 58.827 1508 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 0.00 % 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: -1.93 (0.22), residues: 1324 helix: -0.67 (0.22), residues: 511 sheet: -1.06 (0.41), residues: 150 loop : -1.81 (0.23), residues: 663 *********************** 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 57 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2133 time to fit residues: 19.4667 Evaluate side-chains 49 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7479 ------------------------------------------------------------------------------- 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: 3.9990 chunk 121 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 0.0000 chunk 36 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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** A 20 ASN ** A 132 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 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5104 moved from start: 1.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11152 Z= 0.178 Angle : 0.600 9.045 15096 Z= 0.313 Chirality : 0.042 0.178 1596 Planarity : 0.004 0.045 1946 Dihedral : 6.189 59.334 1508 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.00 % 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: -1.25 (0.23), residues: 1324 helix: 0.10 (0.24), residues: 493 sheet: -0.76 (0.42), residues: 150 loop : -1.54 (0.23), residues: 681 *********************** 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 57 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2103 time to fit residues: 19.1371 Evaluate side-chains 49 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5372 ------------------------------------------------------------------------------- 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: 8.9990 chunk 87 optimal weight: 0.0470 chunk 131 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- 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** A 20 ASN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 68 HIS ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5040 moved from start: 1.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 11152 Z= 0.156 Angle : 0.566 8.970 15096 Z= 0.293 Chirality : 0.041 0.181 1596 Planarity : 0.004 0.045 1946 Dihedral : 5.889 59.648 1508 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.00 % 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: -0.97 (0.23), residues: 1324 helix: 0.40 (0.24), residues: 504 sheet: -0.71 (0.42), residues: 152 loop : -1.45 (0.23), residues: 668 ********************** 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 57 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2123 time to fit residues: 19.3127 Evaluate side-chains 50 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7224 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 0.0020 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 5 optimal weight: 0.0970 chunk 75 optimal weight: 0.0270 overall best weight: 0.5846 ------------------------------------------------------------------------------- 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** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.055717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.039279 restraints weight = 109668.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.040083 restraints weight = 82739.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.041032 restraints weight = 68528.081| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 1.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 11152 Z= 0.135 Angle : 0.542 9.484 15096 Z= 0.277 Chirality : 0.041 0.191 1596 Planarity : 0.004 0.048 1946 Dihedral : 5.536 59.710 1508 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.00 % 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: -0.64 (0.23), residues: 1324 helix: 0.70 (0.24), residues: 503 sheet: -0.42 (0.44), residues: 141 loop : -1.30 (0.23), residues: 680 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1897.11 seconds wall clock time: 36 minutes 5.56 seconds (2165.56 seconds total)