Starting phenix.real_space_refine on Tue Nov 21 19:46:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sid_40506/11_2023/8sid_40506_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sid_40506/11_2023/8sid_40506.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sid_40506/11_2023/8sid_40506_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sid_40506/11_2023/8sid_40506_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sid_40506/11_2023/8sid_40506_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sid_40506/11_2023/8sid_40506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sid_40506/11_2023/8sid_40506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sid_40506/11_2023/8sid_40506_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sid_40506/11_2023/8sid_40506_trim_updated.pdb" } resolution = 2.71 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= 0.003 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 98 5.16 5 C 11520 2.51 5 N 2837 2.21 5 O 3310 1.98 5 H 16960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 34733 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5473 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5454 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5473 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5454 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5443 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1573 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1784 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1595 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1798 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'ABU': 1, 'NAG': 1, 'ZWY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {'ABU': 1, 'NAG': 1, 'Q3G': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 175 Unusual residues: {'POV': 1, 'PTY': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 13.86, per 1000 atoms: 0.40 Number of scatterers: 34733 At special positions: 0 Unit cell: (133.675, 160.41, 100.524, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 8 15.00 O 3310 8.00 N 2837 7.00 C 11520 6.00 H 16960 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 401 " - " ASN A 80 " " NAG C 401 " - " ASN C 80 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 29.23 Conformation dependent library (CDL) restraints added in 3.6 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 30 sheets defined 28.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 227 through 240 removed outlier: 4.348A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.783A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 304 Processing helix chain 'A' and resid 310 through 339 removed outlier: 3.921A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 224 through 245 removed outlier: 3.570A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 3.958A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 275 removed outlier: 3.663A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 345 removed outlier: 3.981A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.521A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 removed outlier: 3.536A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 338 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 245 removed outlier: 4.504A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 4.112A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 274 Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 345 removed outlier: 4.174A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 235 through 239 Processing helix chain 'E' and resid 241 through 255 removed outlier: 3.900A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 286 Processing helix chain 'E' and resid 295 through 323 removed outlier: 3.553A pdb=" N PHE E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 356 removed outlier: 3.824A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.459A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 64 through 68 Processing sheet with id= C, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.826A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= E, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.195A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 179 through 181 removed outlier: 6.518A pdb=" N ILE B 45 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= H, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.806A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.519A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.857A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 39 through 43 Processing sheet with id= L, first strand: chain 'D' and resid 179 through 181 removed outlier: 6.575A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.257A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= O, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.886A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 179 through 183 removed outlier: 5.919A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.518A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 116 through 121 removed outlier: 6.997A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= T, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.018A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.053A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= W, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.528A pdb=" N TRP J 36 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 68 through 73 Processing sheet with id= Y, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= Z, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.027A pdb=" N LYS L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.113A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.578A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.599A pdb=" N SER K 117 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.833A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS K 99 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 2016 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: 12.62 Time building geometry restraints manager: 30.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 16951 1.00 - 1.21: 22 1.21 - 1.42: 7601 1.42 - 1.62: 10421 1.62 - 1.83: 167 Bond restraints: 35162 Sorted by residual: bond pdb=" C15 ZWY A 403 " pdb=" C16 ZWY A 403 " ideal model delta sigma weight residual 0.007 1.534 -1.527 2.00e-02 2.50e+03 5.83e+03 bond pdb=" C18 ZWY A 403 " pdb=" C19 ZWY A 403 " ideal model delta sigma weight residual 0.565 1.517 -0.952 2.00e-02 2.50e+03 2.27e+03 bond pdb=" C05 ZWY A 403 " pdb=" C06 ZWY A 403 " ideal model delta sigma weight residual 0.767 1.541 -0.774 2.00e-02 2.50e+03 1.50e+03 bond pdb=" C02 ZWY A 403 " pdb=" C03 ZWY A 403 " ideal model delta sigma weight residual 0.870 1.531 -0.661 2.00e-02 2.50e+03 1.09e+03 bond pdb=" C14 ZWY A 403 " pdb=" C15 ZWY A 403 " ideal model delta sigma weight residual 2.172 1.516 0.656 2.00e-02 2.50e+03 1.07e+03 ... (remaining 35157 not shown) Histogram of bond angle deviations from ideal: 89.88 - 102.22: 84 102.22 - 114.56: 42702 114.56 - 126.90: 19933 126.90 - 139.23: 241 139.23 - 151.57: 3 Bond angle restraints: 62963 Sorted by residual: angle pdb=" C13 ZWY A 403 " pdb=" C14 ZWY A 403 " pdb=" C19 ZWY A 403 " ideal model delta sigma weight residual 169.18 120.71 48.47 3.00e+00 1.11e-01 2.61e+02 angle pdb=" C13 ZWY A 403 " pdb=" C14 ZWY A 403 " pdb=" C15 ZWY A 403 " ideal model delta sigma weight residual 80.34 122.31 -41.97 3.00e+00 1.11e-01 1.96e+02 angle pdb=" C14 ZWY A 403 " pdb=" C15 ZWY A 403 " pdb=" C25 ZWY A 403 " ideal model delta sigma weight residual 70.53 108.58 -38.05 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C05 ZWY A 403 " pdb=" C15 ZWY A 403 " pdb=" C25 ZWY A 403 " ideal model delta sigma weight residual 74.41 111.74 -37.33 3.00e+00 1.11e-01 1.55e+02 angle pdb=" C16 ZWY A 403 " pdb=" C15 ZWY A 403 " pdb=" C25 ZWY A 403 " ideal model delta sigma weight residual 76.63 110.44 -33.81 3.00e+00 1.11e-01 1.27e+02 ... (remaining 62958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 13948 33.00 - 66.00: 378 66.00 - 98.99: 24 98.99 - 131.99: 5 131.99 - 164.99: 4 Dihedral angle restraints: 14359 sinusoidal: 6671 harmonic: 7688 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -16.76 -69.24 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CA CYS E 165 " pdb=" C CYS E 165 " pdb=" N PRO E 166 " pdb=" CA PRO E 166 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C3 PTY B 402 " pdb=" O11 PTY B 402 " pdb=" P1 PTY B 402 " pdb=" O12 PTY B 402 " ideal model delta sinusoidal sigma weight residual 300.23 135.24 164.99 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 14356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.889: 2817 0.889 - 1.778: 1 1.778 - 2.667: 1 2.667 - 3.555: 1 3.555 - 4.444: 1 Chirality restraints: 2821 Sorted by residual: chirality pdb=" C06 ZWY A 403 " pdb=" C05 ZWY A 403 " pdb=" C07 ZWY A 403 " pdb=" C12 ZWY A 403 " both_signs ideal model delta sigma weight residual False -1.73 2.72 -4.44 2.00e-01 2.50e+01 4.94e+02 chirality pdb=" C15 ZWY A 403 " pdb=" C05 ZWY A 403 " pdb=" C14 ZWY A 403 " pdb=" C16 ZWY A 403 " both_signs ideal model delta sigma weight residual False -0.02 2.86 -2.88 2.00e-01 2.50e+01 2.08e+02 chirality pdb=" C18 ZWY A 403 " pdb=" C17 ZWY A 403 " pdb=" C19 ZWY A 403 " pdb=" O20 ZWY A 403 " both_signs ideal model delta sigma weight residual False -0.77 -2.63 1.87 2.00e-01 2.50e+01 8.71e+01 ... (remaining 2818 not shown) Planarity restraints: 5033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 ZWY A 403 " -0.184 2.00e-02 2.50e+03 1.53e-01 2.94e+02 pdb=" C13 ZWY A 403 " 0.228 2.00e-02 2.50e+03 pdb=" C14 ZWY A 403 " 0.095 2.00e-02 2.50e+03 pdb=" C15 ZWY A 403 " 0.012 2.00e-02 2.50e+03 pdb=" C19 ZWY A 403 " -0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 148 " 0.062 2.00e-02 2.50e+03 9.66e-02 1.40e+02 pdb=" CD GLN A 148 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN A 148 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 GLN A 148 " -0.162 2.00e-02 2.50e+03 pdb="HE21 GLN A 148 " -0.034 2.00e-02 2.50e+03 pdb="HE22 GLN A 148 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 347 " 0.043 2.00e-02 2.50e+03 8.77e-02 1.15e+02 pdb=" CG ASN E 347 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN E 347 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN E 347 " -0.153 2.00e-02 2.50e+03 pdb="HD21 ASN E 347 " -0.039 2.00e-02 2.50e+03 pdb="HD22 ASN E 347 " 0.139 2.00e-02 2.50e+03 ... (remaining 5030 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1432 2.16 - 2.77: 66637 2.77 - 3.38: 93870 3.38 - 3.99: 129053 3.99 - 4.60: 201162 Nonbonded interactions: 492154 Sorted by model distance: nonbonded pdb=" H GLY K 100 " pdb=" O ALA K 104 " model vdw 1.550 1.850 nonbonded pdb=" OE1 GLU C 155 " pdb="HH21 ARG C 207 " model vdw 1.554 1.850 nonbonded pdb=" OG1 THR D 99 " pdb=" HH TYR D 169 " model vdw 1.557 1.850 nonbonded pdb=" HH TYR I 36 " pdb=" O ALA J 104 " model vdw 1.578 1.850 nonbonded pdb="HE22 GLN L 6 " pdb=" O TYR L 86 " model vdw 1.579 1.850 ... (remaining 492149 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' and (resid 7 through 340 or resid 401 through 402)) selection = (chain 'C' and (resid 7 through 340 or resid 401 through 402)) } ncs_group { reference = (chain 'B' and (resid 10 through 347 or resid 402 through 403)) selection = (chain 'D' and (resid 10 through 347 or (resid 402 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or \ name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 ) \ ) or (resid 403 and (name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C3 or name C30 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 o \ r name C41 or name C42 or name C43 or name C44 or name C5 or name C6 or name C8 \ or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O \ 30 or name O4 or name O7 or name P1 )))) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.470 Extract box with map and model: 6.550 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 108.460 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 : 0.019 1.527 18202 Z= 1.425 Angle : 0.982 48.469 24679 Z= 0.412 Chirality : 0.118 4.444 2821 Planarity : 0.005 0.153 3002 Dihedral : 15.094 164.988 6564 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -2.81 (0.16), residues: 2103 helix: -0.14 (0.20), residues: 573 sheet: -2.58 (0.17), residues: 680 loop : -2.31 (0.18), residues: 850 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.762 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: 0 outliers final: 0 residues processed: 384 average time/residue: 2.8286 time to fit residues: 1217.5307 Evaluate side-chains 205 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.628 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS I 6 GLN I 53 ASN J 5 GLN L 38 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 18202 Z= 0.384 Angle : 0.755 14.217 24679 Z= 0.360 Chirality : 0.048 0.634 2821 Planarity : 0.006 0.163 3002 Dihedral : 13.401 179.186 2624 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 2.12 % Allowed : 11.42 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.59 (0.17), residues: 2103 helix: 1.25 (0.21), residues: 575 sheet: -1.96 (0.18), residues: 683 loop : -1.79 (0.19), residues: 845 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 205 time to evaluate : 2.719 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: 40 outliers final: 16 residues processed: 230 average time/residue: 2.6909 time to fit residues: 699.2023 Evaluate side-chains 204 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 2.774 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.4568 time to fit residues: 4.9348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 18202 Z= 0.384 Angle : 0.755 14.212 24679 Z= 0.360 Chirality : 0.047 0.628 2821 Planarity : 0.006 0.163 3002 Dihedral : 13.413 179.185 2624 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 0.80 % Allowed : 13.38 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.59 (0.17), residues: 2103 helix: 1.25 (0.21), residues: 575 sheet: -1.96 (0.18), residues: 683 loop : -1.78 (0.19), residues: 845 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 3.041 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: 15 outliers final: 14 residues processed: 203 average time/residue: 2.6586 time to fit residues: 615.2337 Evaluate side-chains 203 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 189 time to evaluate : 2.904 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 3.9152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 18202 Z= 0.374 Angle : 0.762 16.921 24679 Z= 0.361 Chirality : 0.047 0.552 2821 Planarity : 0.006 0.163 3002 Dihedral : 13.364 179.167 2624 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 0.80 % Allowed : 13.44 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2103 helix: 1.29 (0.21), residues: 573 sheet: -1.96 (0.18), residues: 683 loop : -1.76 (0.19), residues: 847 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 2.722 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: 15 outliers final: 15 residues processed: 204 average time/residue: 2.6799 time to fit residues: 619.5874 Evaluate side-chains 203 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 3.121 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 3.9647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 0.0770 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 18202 Z= 0.334 Angle : 0.660 8.956 24679 Z= 0.328 Chirality : 0.045 0.415 2821 Planarity : 0.005 0.151 3002 Dihedral : 13.177 179.619 2624 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.49 % Allowed : 12.64 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.43 (0.17), residues: 2103 helix: 1.39 (0.21), residues: 575 sheet: -1.88 (0.18), residues: 684 loop : -1.69 (0.19), residues: 844 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 2.876 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: 28 outliers final: 20 residues processed: 209 average time/residue: 2.6551 time to fit residues: 628.2342 Evaluate side-chains 209 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 2.576 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.4452 time to fit residues: 5.4733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 18202 Z= 0.339 Angle : 0.654 10.894 24679 Z= 0.324 Chirality : 0.045 0.488 2821 Planarity : 0.005 0.150 3002 Dihedral : 13.165 179.458 2624 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.06 % Allowed : 13.12 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.42 (0.17), residues: 2103 helix: 1.40 (0.21), residues: 575 sheet: -1.88 (0.18), residues: 684 loop : -1.67 (0.19), residues: 844 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 2.887 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 outliers start: 20 outliers final: 19 residues processed: 206 average time/residue: 2.6290 time to fit residues: 616.1269 Evaluate side-chains 208 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 2.642 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 3 average time/residue: 2.1116 time to fit residues: 10.6307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 18202 Z= 0.339 Angle : 0.654 10.894 24679 Z= 0.324 Chirality : 0.045 0.488 2821 Planarity : 0.005 0.150 3002 Dihedral : 13.166 179.458 2624 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.85 % Allowed : 13.44 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.42 (0.17), residues: 2103 helix: 1.40 (0.21), residues: 575 sheet: -1.88 (0.18), residues: 684 loop : -1.67 (0.19), residues: 844 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 2.834 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: 16 outliers final: 16 residues processed: 205 average time/residue: 2.6007 time to fit residues: 604.1910 Evaluate side-chains 205 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 2.757 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 3.3299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 18202 Z= 0.339 Angle : 0.654 10.887 24679 Z= 0.324 Chirality : 0.045 0.488 2821 Planarity : 0.005 0.150 3002 Dihedral : 13.167 179.458 2624 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.85 % Allowed : 13.44 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.42 (0.17), residues: 2103 helix: 1.40 (0.21), residues: 575 sheet: -1.88 (0.18), residues: 684 loop : -1.67 (0.19), residues: 844 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 2.906 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: 16 outliers final: 16 residues processed: 205 average time/residue: 2.6555 time to fit residues: 621.9113 Evaluate side-chains 205 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 3.027 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 3.7117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 18202 Z= 0.338 Angle : 0.655 10.527 24679 Z= 0.324 Chirality : 0.045 0.484 2821 Planarity : 0.005 0.151 3002 Dihedral : 13.154 179.456 2624 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.85 % Allowed : 13.44 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.42 (0.17), residues: 2103 helix: 1.40 (0.21), residues: 575 sheet: -1.88 (0.18), residues: 684 loop : -1.67 (0.19), residues: 844 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 2.975 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: 16 outliers final: 16 residues processed: 205 average time/residue: 2.5521 time to fit residues: 594.5193 Evaluate side-chains 205 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 2.5869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 206 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: