Starting phenix.real_space_refine on Wed Feb 21 16:46:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/02_2024/7t0z_25585_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/02_2024/7t0z_25585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/02_2024/7t0z_25585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/02_2024/7t0z_25585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/02_2024/7t0z_25585_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/02_2024/7t0z_25585_trim_updated.pdb" } resolution = 3.0 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: 5 Type Number sf(0) Gaussians S 86 5.16 5 C 10215 2.51 5 N 2568 2.21 5 O 2912 1.98 5 H 15348 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31129 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5471 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 5448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5448 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5470 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 5447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5447 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 5447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5447 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 319} Chain: "H" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1862 Classifications: {'peptide': 125} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1664 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "F" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.70, per 1000 atoms: 0.47 Number of scatterers: 31129 At special positions: 0 Unit cell: (145.665, 114.374, 132.717, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 O 2912 8.00 N 2568 7.00 C 10215 6.00 H 15348 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN M 8 " - " MAN M 9 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG D 401 " - " ASN D 111 " Time building additional restraints: 28.67 Conformation dependent library (CDL) restraints added in 3.4 seconds 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 22 sheets defined 32.6% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 219 through 241 removed outlier: 4.854A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 3.846A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 Processing helix chain 'A' and resid 280 through 306 Processing helix chain 'A' and resid 310 through 338 Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 23 removed outlier: 4.335A pdb=" N LEU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) 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 88 through 91 No H-bonds generated for 'chain 'B' and resid 88 through 91' 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: 5.086A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.000A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 removed outlier: 3.550A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 344 Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 219 through 240 removed outlier: 5.404A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.796A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 4.289A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 305 Processing helix chain 'C' and resid 310 through 338 removed outlier: 3.553A pdb=" N ALA C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' 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 246 removed outlier: 5.416A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 4.487A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 346 Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 235 through 255 Proline residue: E 243 - end of helix removed outlier: 3.750A pdb=" N SER E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 281 removed outlier: 3.838A pdb=" N THR E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 320 Processing helix chain 'E' and resid 325 through 356 removed outlier: 3.608A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.323A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.950A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.740A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.280A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= F, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 150 through 154 removed outlier: 4.011A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.349A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.618A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 203 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.721A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.472A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= M, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.514A pdb=" N PHE D 217 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 179 through 183 removed outlier: 6.252A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 57 through 59 Processing sheet with id= P, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.621A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.571A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= S, first strand: chain 'H' and resid 118 through 120 removed outlier: 6.106A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= U, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.508A pdb=" N LYS L 104 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU L 13 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU L 106 " --> pdb=" O LEU L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'L' and resid 97 through 99 removed outlier: 6.185A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 2085 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: 11.38 Time building geometry restraints manager: 29.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14880 1.03 - 1.23: 1305 1.23 - 1.43: 6255 1.43 - 1.63: 8942 1.63 - 1.83: 149 Bond restraints: 31531 Sorted by residual: bond pdb=" N TYR A 205 " pdb=" H TYR A 205 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" N ARG L 91 " pdb=" H ARG L 91 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N TYR L 97 " pdb=" H TYR L 97 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N THR B 130 " pdb=" H THR B 130 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N PHE B 65 " pdb=" H PHE B 65 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 31526 not shown) Histogram of bond angle deviations from ideal: 97.63 - 104.97: 281 104.97 - 112.30: 35393 112.30 - 119.64: 8410 119.64 - 126.98: 12358 126.98 - 134.32: 203 Bond angle restraints: 56645 Sorted by residual: angle pdb=" N THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 110.65 102.42 8.23 1.47e+00 4.63e-01 3.13e+01 angle pdb=" C THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 109.55 118.14 -8.59 1.68e+00 3.54e-01 2.61e+01 angle pdb=" CA VAL H 104 " pdb=" C VAL H 104 " pdb=" O VAL H 104 " ideal model delta sigma weight residual 121.92 116.93 4.99 1.17e+00 7.31e-01 1.82e+01 angle pdb=" CA PRO C 206 " pdb=" C PRO C 206 " pdb=" O PRO C 206 " ideal model delta sigma weight residual 121.98 116.78 5.20 1.23e+00 6.61e-01 1.79e+01 angle pdb=" CA GLU C 155 " pdb=" C GLU C 155 " pdb=" O GLU C 155 " ideal model delta sigma weight residual 121.58 116.87 4.71 1.16e+00 7.43e-01 1.65e+01 ... (remaining 56640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 14390 21.62 - 43.24: 690 43.24 - 64.86: 156 64.86 - 86.48: 36 86.48 - 108.10: 14 Dihedral angle restraints: 15286 sinusoidal: 8334 harmonic: 6952 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 -30.53 -55.47 1 1.00e+01 1.00e-02 4.16e+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 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ARG D 37 " pdb=" C ARG D 37 " pdb=" N VAL D 38 " pdb=" CA VAL D 38 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 15283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2049 0.056 - 0.113: 432 0.113 - 0.169: 62 0.169 - 0.225: 4 0.225 - 0.281: 3 Chirality restraints: 2550 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2547 not shown) Planarity restraints: 4529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 303 " 0.170 2.00e-02 2.50e+03 4.99e-01 3.74e+03 pdb=" CG ASN A 303 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 303 " -0.167 2.00e-02 2.50e+03 pdb=" ND2 ASN A 303 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 303 " -0.842 2.00e-02 2.50e+03 pdb="HD22 ASN A 303 " 0.854 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 238 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C ILE E 238 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE E 238 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN E 239 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 155 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C GLU C 155 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU C 155 " -0.016 2.00e-02 2.50e+03 pdb=" N SER C 156 " -0.015 2.00e-02 2.50e+03 ... (remaining 4526 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 979 2.15 - 2.76: 58879 2.76 - 3.37: 87049 3.37 - 3.99: 117640 3.99 - 4.60: 182250 Nonbonded interactions: 446797 Sorted by model distance: nonbonded pdb=" O ASP B 145 " pdb=" H MET B 148 " model vdw 1.533 1.850 nonbonded pdb=" O SER B 92 " pdb="HH12 ARG C 86 " model vdw 1.559 1.850 nonbonded pdb=" HH TYR B 60 " pdb=" O PRO B 154 " model vdw 1.580 1.850 nonbonded pdb=" OD1 ASP A 101 " pdb="HH22 ARG B 132 " model vdw 1.582 1.850 nonbonded pdb=" OE1 GLU D 59 " pdb=" HZ2 LYS D 105 " model vdw 1.583 1.850 ... (remaining 446792 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 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 150 through 340)) selection = (chain 'C' and resid 7 through 340) } ncs_group { reference = (chain 'B' and (resid 10 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 112 through 347)) selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } 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: 1.390 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: 0.430 Extract box with map and model: 6.600 Check model and map are aligned: 0.450 Set scattering table: 0.290 Process input model: 104.980 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.006 0.087 16183 Z= 0.403 Angle : 0.743 10.463 22014 Z= 0.411 Chirality : 0.048 0.281 2550 Planarity : 0.005 0.049 2705 Dihedral : 14.331 108.098 6183 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: -0.22 (0.19), residues: 1898 helix: 1.48 (0.20), residues: 621 sheet: -0.78 (0.22), residues: 540 loop : -0.97 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 246 HIS 0.005 0.001 HIS C 267 PHE 0.022 0.002 PHE D 258 TYR 0.029 0.002 TYR C 299 ARG 0.006 0.001 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 THR cc_start: 0.8798 (t) cc_final: 0.7741 (t) REVERT: D 20 ASP cc_start: 0.8115 (m-30) cc_final: 0.7853 (m-30) REVERT: D 131 MET cc_start: 0.8553 (mtp) cc_final: 0.8222 (mtp) REVERT: D 190 GLN cc_start: 0.8162 (pt0) cc_final: 0.7306 (pm20) REVERT: E 99 ASN cc_start: 0.8120 (m110) cc_final: 0.7819 (m-40) REVERT: E 162 GLU cc_start: 0.6620 (tm-30) cc_final: 0.6175 (tm-30) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 2.6592 time to fit residues: 974.0418 Evaluate side-chains 254 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16183 Z= 0.189 Angle : 0.569 10.023 22014 Z= 0.295 Chirality : 0.042 0.155 2550 Planarity : 0.004 0.063 2705 Dihedral : 8.483 73.653 2619 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.47 % Allowed : 9.47 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.22 (0.19), residues: 1898 helix: 1.72 (0.20), residues: 627 sheet: -0.41 (0.22), residues: 520 loop : -0.72 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 246 HIS 0.003 0.001 HIS E 122 PHE 0.014 0.001 PHE D 304 TYR 0.028 0.001 TYR C 299 ARG 0.008 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 332 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6169 (mp) REVERT: C 274 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7158 (mmtt) REVERT: C 294 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7040 (mpt) REVERT: D 16 THR cc_start: 0.8688 (t) cc_final: 0.7596 (t) REVERT: D 17 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6909 (mtm110) REVERT: D 78 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6613 (tmmt) REVERT: D 112 MET cc_start: 0.8076 (ttp) cc_final: 0.7858 (ttp) REVERT: D 131 MET cc_start: 0.8481 (mtp) cc_final: 0.8228 (mtp) REVERT: D 190 GLN cc_start: 0.8164 (pt0) cc_final: 0.7283 (pm20) REVERT: E 162 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6373 (tm-30) REVERT: E 214 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8308 (mtmm) outliers start: 25 outliers final: 11 residues processed: 282 average time/residue: 2.4164 time to fit residues: 763.7100 Evaluate side-chains 266 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 170 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 57 optimal weight: 0.0030 chunk 136 optimal weight: 3.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16183 Z= 0.229 Angle : 0.544 9.592 22014 Z= 0.283 Chirality : 0.042 0.153 2550 Planarity : 0.004 0.050 2705 Dihedral : 7.194 67.059 2619 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.53 % Allowed : 11.24 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.36 (0.19), residues: 1898 helix: 1.90 (0.20), residues: 621 sheet: -0.13 (0.23), residues: 515 loop : -0.85 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 246 HIS 0.004 0.001 HIS C 267 PHE 0.014 0.001 PHE H 106 TYR 0.029 0.001 TYR C 299 ARG 0.005 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.8169 (mtm) cc_final: 0.7934 (mtp) REVERT: B 279 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6920 (mptp) REVERT: B 312 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6852 (tptm) REVERT: B 332 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6218 (mp) REVERT: C 207 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8301 (ttm-80) REVERT: C 274 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7191 (mmtt) REVERT: C 294 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7066 (mpt) REVERT: D 131 MET cc_start: 0.8521 (mtp) cc_final: 0.8320 (mtp) REVERT: D 190 GLN cc_start: 0.8183 (pt0) cc_final: 0.7288 (pm20) REVERT: D 294 TYR cc_start: 0.7351 (t80) cc_final: 0.6971 (t80) REVERT: E 162 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6594 (tm-30) REVERT: E 214 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8350 (mtmm) outliers start: 26 outliers final: 14 residues processed: 275 average time/residue: 2.3859 time to fit residues: 737.4519 Evaluate side-chains 261 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16183 Z= 0.232 Angle : 0.537 10.165 22014 Z= 0.279 Chirality : 0.041 0.179 2550 Planarity : 0.004 0.051 2705 Dihedral : 6.577 59.353 2619 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.82 % Allowed : 12.12 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.47 (0.19), residues: 1898 helix: 1.99 (0.20), residues: 621 sheet: -0.03 (0.23), residues: 515 loop : -0.82 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 241 HIS 0.004 0.001 HIS C 267 PHE 0.013 0.001 PHE B 336 TYR 0.027 0.001 TYR C 299 ARG 0.003 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 260 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.8175 (mtm) cc_final: 0.7942 (mtp) REVERT: B 279 LYS cc_start: 0.7220 (mmmt) cc_final: 0.6958 (mptp) REVERT: B 326 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5892 (ttt-90) REVERT: B 332 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6259 (mp) REVERT: C 274 LYS cc_start: 0.7613 (mmtm) cc_final: 0.7177 (mmtt) REVERT: C 294 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7009 (mpt) REVERT: D 78 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6702 (tmmt) REVERT: D 131 MET cc_start: 0.8521 (mtp) cc_final: 0.8261 (mtp) REVERT: D 190 GLN cc_start: 0.8191 (pt0) cc_final: 0.7284 (pm20) REVERT: D 294 TYR cc_start: 0.7271 (t80) cc_final: 0.6829 (t80) REVERT: E 162 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6452 (tm-30) REVERT: E 209 THR cc_start: 0.8576 (m) cc_final: 0.8373 (p) REVERT: E 214 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8365 (mtmm) outliers start: 31 outliers final: 17 residues processed: 273 average time/residue: 2.3338 time to fit residues: 717.0159 Evaluate side-chains 271 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.0270 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN E 154 GLN L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16183 Z= 0.204 Angle : 0.523 9.462 22014 Z= 0.271 Chirality : 0.041 0.195 2550 Planarity : 0.004 0.051 2705 Dihedral : 6.109 53.144 2619 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.88 % Allowed : 12.47 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.55 (0.19), residues: 1898 helix: 2.10 (0.20), residues: 621 sheet: -0.11 (0.22), residues: 532 loop : -0.72 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 67 HIS 0.004 0.001 HIS C 267 PHE 0.013 0.001 PHE E 308 TYR 0.029 0.001 TYR C 299 ARG 0.004 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 257 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 LYS cc_start: 0.7192 (mmmt) cc_final: 0.6937 (mptp) REVERT: B 332 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6283 (mp) REVERT: C 274 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7193 (mmtt) REVERT: C 294 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7122 (mpt) REVERT: D 78 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6534 (tmmt) REVERT: D 131 MET cc_start: 0.8522 (mtp) cc_final: 0.8289 (mtp) REVERT: D 190 GLN cc_start: 0.8188 (pt0) cc_final: 0.7276 (pm20) REVERT: E 162 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6582 (tm-30) REVERT: E 214 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8365 (mtmm) REVERT: E 284 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7567 (mtt-85) outliers start: 32 outliers final: 16 residues processed: 276 average time/residue: 2.3413 time to fit residues: 728.4085 Evaluate side-chains 267 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 246 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 284 ARG Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN L 42 GLN L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16183 Z= 0.361 Angle : 0.589 10.181 22014 Z= 0.305 Chirality : 0.043 0.198 2550 Planarity : 0.005 0.051 2705 Dihedral : 6.384 55.082 2619 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.18 % Allowed : 12.65 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.39 (0.19), residues: 1898 helix: 1.94 (0.20), residues: 621 sheet: -0.17 (0.22), residues: 558 loop : -0.83 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 246 HIS 0.004 0.001 HIS C 267 PHE 0.017 0.002 PHE B 336 TYR 0.028 0.002 TYR C 299 ARG 0.005 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 249 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 279 LYS cc_start: 0.7362 (mmmt) cc_final: 0.7082 (mptp) REVERT: B 312 LYS cc_start: 0.7861 (tmtt) cc_final: 0.7643 (tptm) REVERT: B 332 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6373 (mp) REVERT: C 274 LYS cc_start: 0.7509 (mmtm) cc_final: 0.7290 (mmtt) REVERT: C 294 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7144 (mpt) REVERT: D 78 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6632 (tmmt) REVERT: D 131 MET cc_start: 0.8546 (mtp) cc_final: 0.8320 (mtp) REVERT: D 190 GLN cc_start: 0.8200 (pt0) cc_final: 0.7284 (pm20) REVERT: E 162 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6558 (tm-30) REVERT: E 214 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8370 (mtmm) REVERT: E 242 ILE cc_start: 0.7079 (mp) cc_final: 0.6877 (mt) REVERT: E 284 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7500 (mtt-85) outliers start: 37 outliers final: 22 residues processed: 267 average time/residue: 2.4196 time to fit residues: 727.1256 Evaluate side-chains 267 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 284 ARG Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 180 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16183 Z= 0.234 Angle : 0.540 10.045 22014 Z= 0.279 Chirality : 0.041 0.208 2550 Planarity : 0.004 0.052 2705 Dihedral : 5.989 50.797 2619 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.88 % Allowed : 13.71 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.52 (0.19), residues: 1898 helix: 2.04 (0.20), residues: 621 sheet: -0.11 (0.22), residues: 533 loop : -0.72 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 246 HIS 0.004 0.001 HIS C 267 PHE 0.013 0.001 PHE E 308 TYR 0.027 0.001 TYR C 299 ARG 0.002 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: B 279 LYS cc_start: 0.7245 (mmmt) cc_final: 0.6932 (mptp) REVERT: B 312 LYS cc_start: 0.7973 (tmtt) cc_final: 0.7669 (tptm) REVERT: B 332 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6339 (mp) REVERT: C 17 ASP cc_start: 0.7412 (m-30) cc_final: 0.7178 (m-30) REVERT: C 294 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7141 (mpt) REVERT: D 190 GLN cc_start: 0.8189 (pt0) cc_final: 0.7287 (pm20) REVERT: D 228 ILE cc_start: 0.8306 (tp) cc_final: 0.8093 (mm) REVERT: D 246 TRP cc_start: 0.7756 (m100) cc_final: 0.7514 (m-90) REVERT: E 162 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6648 (tm-30) REVERT: E 209 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8561 (p) REVERT: E 214 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8363 (mtmm) REVERT: E 284 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7529 (mtt-85) outliers start: 32 outliers final: 19 residues processed: 265 average time/residue: 2.4042 time to fit residues: 716.0128 Evaluate side-chains 266 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 241 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 284 ARG Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16183 Z= 0.266 Angle : 0.549 9.928 22014 Z= 0.283 Chirality : 0.042 0.211 2550 Planarity : 0.004 0.049 2705 Dihedral : 5.908 52.318 2619 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.29 % Allowed : 13.65 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.54 (0.19), residues: 1898 helix: 2.07 (0.20), residues: 621 sheet: -0.08 (0.22), residues: 533 loop : -0.72 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 246 HIS 0.004 0.001 HIS C 267 PHE 0.013 0.001 PHE H 106 TYR 0.028 0.002 TYR C 299 ARG 0.004 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 245 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: B 279 LYS cc_start: 0.7359 (mmmt) cc_final: 0.7101 (mptp) REVERT: B 317 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.5196 (ttm-80) REVERT: B 332 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6369 (mp) REVERT: C 17 ASP cc_start: 0.7418 (m-30) cc_final: 0.7104 (m-30) REVERT: C 294 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7169 (mpt) REVERT: D 78 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6538 (tmmt) REVERT: D 190 GLN cc_start: 0.8182 (pt0) cc_final: 0.7280 (pm20) REVERT: D 228 ILE cc_start: 0.8316 (tp) cc_final: 0.8095 (mm) REVERT: D 246 TRP cc_start: 0.7746 (m100) cc_final: 0.7507 (m-90) REVERT: E 162 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6638 (tm-30) REVERT: E 209 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8571 (p) REVERT: E 214 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: E 284 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7525 (mtt-85) outliers start: 39 outliers final: 24 residues processed: 264 average time/residue: 2.4379 time to fit residues: 722.7981 Evaluate side-chains 276 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 244 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 284 ARG Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16183 Z= 0.208 Angle : 0.528 9.876 22014 Z= 0.272 Chirality : 0.041 0.216 2550 Planarity : 0.004 0.051 2705 Dihedral : 5.643 53.280 2619 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.82 % Allowed : 14.59 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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 (0.19), residues: 1898 helix: 2.18 (0.20), residues: 619 sheet: -0.03 (0.22), residues: 530 loop : -0.70 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 67 HIS 0.003 0.001 HIS E 122 PHE 0.013 0.001 PHE B 15 TYR 0.028 0.001 TYR C 299 ARG 0.004 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 249 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 LYS cc_start: 0.7307 (mmmt) cc_final: 0.7030 (mptp) REVERT: B 332 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6350 (mp) REVERT: C 294 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7170 (mpt) REVERT: D 78 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6508 (tmmt) REVERT: D 190 GLN cc_start: 0.8170 (pt0) cc_final: 0.7271 (pm20) REVERT: D 228 ILE cc_start: 0.8291 (tp) cc_final: 0.8060 (mm) REVERT: E 162 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6629 (tm-30) REVERT: E 209 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8571 (p) REVERT: E 214 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: E 284 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7488 (mtt-85) outliers start: 31 outliers final: 21 residues processed: 263 average time/residue: 2.4120 time to fit residues: 714.8297 Evaluate side-chains 268 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 241 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 284 ARG Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN L 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16183 Z= 0.262 Angle : 0.548 9.748 22014 Z= 0.281 Chirality : 0.041 0.218 2550 Planarity : 0.004 0.050 2705 Dihedral : 5.674 54.606 2619 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.82 % Allowed : 15.00 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.62 (0.19), residues: 1898 helix: 2.13 (0.20), residues: 619 sheet: -0.01 (0.23), residues: 523 loop : -0.69 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 246 HIS 0.004 0.001 HIS C 267 PHE 0.013 0.001 PHE E 308 TYR 0.030 0.002 TYR C 299 ARG 0.004 0.000 ARG C 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 248 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 LYS cc_start: 0.7368 (mmmt) cc_final: 0.7100 (mptp) REVERT: B 332 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6366 (mp) REVERT: C 294 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7169 (mpt) REVERT: D 190 GLN cc_start: 0.8175 (pt0) cc_final: 0.7281 (pm20) REVERT: E 162 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6667 (tm-30) REVERT: E 209 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8574 (p) REVERT: E 214 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8378 (mtmm) REVERT: E 284 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7517 (mtt-85) outliers start: 31 outliers final: 21 residues processed: 265 average time/residue: 2.3655 time to fit residues: 705.0271 Evaluate side-chains 270 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 244 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 284 ARG Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097950 restraints weight = 58854.035| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.76 r_work: 0.2900 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16183 Z= 0.186 Angle : 0.526 9.750 22014 Z= 0.270 Chirality : 0.041 0.216 2550 Planarity : 0.004 0.051 2705 Dihedral : 5.417 55.623 2619 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 15.35 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.71 (0.19), residues: 1898 helix: 2.22 (0.20), residues: 619 sheet: 0.02 (0.23), residues: 522 loop : -0.62 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 67 HIS 0.003 0.001 HIS E 122 PHE 0.019 0.001 PHE B 336 TYR 0.029 0.001 TYR C 299 ARG 0.004 0.000 ARG C 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12199.76 seconds wall clock time: 214 minutes 27.15 seconds (12867.15 seconds total)