Starting phenix.real_space_refine on Wed Feb 14 05:28:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihf_35443/02_2024/8ihf_35443_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihf_35443/02_2024/8ihf_35443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihf_35443/02_2024/8ihf_35443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihf_35443/02_2024/8ihf_35443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihf_35443/02_2024/8ihf_35443_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihf_35443/02_2024/8ihf_35443_updated.pdb" } resolution = 2.97 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= -0.001 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5563 2.51 5 N 1473 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 272": "OD1" <-> "OD2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 221": "OD1" <-> "OD2" Residue "R TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1690 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2485 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 383 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2385 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'FI7': 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 Time building chain proxies: 5.25, per 1000 atoms: 0.60 Number of scatterers: 8691 At special positions: 0 Unit cell: (85.49, 117.03, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1594 8.00 N 1473 7.00 C 5563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.05 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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 NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 15 sheets defined 33.4% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.534A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.895A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.732A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'R' and resid 24 through 54 removed outlier: 3.520A pdb=" N LYS R 28 " --> pdb=" O PHE R 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL R 29 " --> pdb=" O ILE R 26 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU R 30 " --> pdb=" O VAL R 27 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.812A pdb=" N LEU R 34 " --> pdb=" O PRO R 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU R 37 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE R 39 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE R 40 " --> pdb=" O GLU R 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU R 42 " --> pdb=" O ILE R 39 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN R 45 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY R 46 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE R 54 " --> pdb=" O ILE R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 88 removed outlier: 3.807A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 98 through 129 removed outlier: 5.033A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 158 Processing helix chain 'R' and resid 160 through 163 Processing helix chain 'R' and resid 191 through 217 removed outlier: 4.133A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 4.095A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 260 removed outlier: 3.502A pdb=" N VAL R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.505A pdb=" N ARG R 251 " --> pdb=" O SER R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 294 removed outlier: 3.794A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR R 283 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.517A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.530A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 33 through 35 Processing sheet with id= D, first strand: chain 'S' and resid 38 through 40 Processing sheet with id= E, first strand: chain 'S' and resid 49 through 51 Processing sheet with id= F, first strand: chain 'S' and resid 156 through 160 Processing sheet with id= G, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.594A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.864A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.798A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.709A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.520A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.514A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.744A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.732A pdb=" N ILE R 169 " --> pdb=" O LEU R 176 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1794 1.33 - 1.46: 2819 1.46 - 1.59: 4189 1.59 - 1.72: 0 1.72 - 1.85: 86 Bond restraints: 8888 Sorted by residual: bond pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.37e-02 5.33e+03 8.29e+00 bond pdb=" C CYS B 233 " pdb=" O CYS B 233 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.24e-02 6.50e+03 7.64e+00 bond pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 1.521 1.489 0.032 1.19e-02 7.06e+03 7.21e+00 bond pdb=" N15 FI7 R 602 " pdb=" O16 FI7 R 602 " ideal model delta sigma weight residual 1.363 1.415 -0.052 2.00e-02 2.50e+03 6.87e+00 bond pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 1.521 1.488 0.033 1.28e-02 6.10e+03 6.45e+00 ... (remaining 8883 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.70: 189 106.70 - 113.53: 4878 113.53 - 120.36: 3161 120.36 - 127.19: 3741 127.19 - 134.02: 100 Bond angle restraints: 12069 Sorted by residual: angle pdb=" C LYS R 166 " pdb=" N MET R 167 " pdb=" CA MET R 167 " ideal model delta sigma weight residual 122.28 117.33 4.95 1.02e+00 9.61e-01 2.36e+01 angle pdb=" CA MET R 167 " pdb=" CB MET R 167 " pdb=" CG MET R 167 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 110.26 105.01 5.25 1.49e+00 4.50e-01 1.24e+01 angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 112.45 116.75 -4.30 1.39e+00 5.18e-01 9.59e+00 angle pdb=" N TRP R 188 " pdb=" CA TRP R 188 " pdb=" C TRP R 188 " ideal model delta sigma weight residual 110.53 106.74 3.79 1.32e+00 5.74e-01 8.25e+00 ... (remaining 12064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 4774 24.88 - 49.75: 395 49.75 - 74.63: 49 74.63 - 99.50: 8 99.50 - 124.38: 1 Dihedral angle restraints: 5227 sinusoidal: 1951 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual -86.00 -41.94 -44.06 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA CYS R 183 " pdb=" C CYS R 183 " pdb=" N HIS R 184 " pdb=" CA HIS R 184 " ideal model delta harmonic sigma weight residual -180.00 -155.09 -24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 897 0.032 - 0.063: 327 0.063 - 0.094: 92 0.094 - 0.126: 56 0.126 - 0.157: 5 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CG LEU S 165 " pdb=" CB LEU S 165 " pdb=" CD1 LEU S 165 " pdb=" CD2 LEU S 165 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA PRO R 81 " pdb=" N PRO R 81 " pdb=" C PRO R 81 " pdb=" CB PRO R 81 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1374 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " -0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO R 81 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C07 FI7 R 602 " 0.032 2.00e-02 2.50e+03 1.71e-02 5.84e+00 pdb=" C08 FI7 R 602 " -0.011 2.00e-02 2.50e+03 pdb=" C09 FI7 R 602 " -0.013 2.00e-02 2.50e+03 pdb=" C10 FI7 R 602 " -0.009 2.00e-02 2.50e+03 pdb=" C11 FI7 R 602 " -0.001 2.00e-02 2.50e+03 pdb=" C13 FI7 R 602 " -0.009 2.00e-02 2.50e+03 pdb=" N14 FI7 R 602 " -0.015 2.00e-02 2.50e+03 pdb=" O12 FI7 R 602 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO S 75 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.032 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1285 2.75 - 3.29: 8079 3.29 - 3.83: 14208 3.83 - 4.36: 17441 4.36 - 4.90: 30369 Nonbonded interactions: 71382 Sorted by model distance: nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.218 2.520 nonbonded pdb=" OD1 ASN A 241 " pdb=" ND1 HIS A 244 " model vdw 2.232 2.520 nonbonded pdb=" NE2 GLN R 170 " pdb=" O GLY R 172 " model vdw 2.233 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR R 284 " pdb=" O23 FI7 R 602 " model vdw 2.260 2.440 ... (remaining 71377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.010 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: 0.000 Extract box with map and model: 5.440 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.720 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.003 0.052 8888 Z= 0.221 Angle : 0.527 7.211 12069 Z= 0.288 Chirality : 0.040 0.157 1377 Planarity : 0.004 0.073 1522 Dihedral : 17.370 124.381 3100 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.11 % Allowed : 26.25 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1115 helix: 0.54 (0.28), residues: 371 sheet: 0.10 (0.33), residues: 258 loop : -1.07 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 188 HIS 0.009 0.001 HIS R 161 PHE 0.013 0.001 PHE R 10 TYR 0.018 0.001 TYR S 235 ARG 0.010 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.946 Fit side-chains REVERT: A 247 MET cc_start: 0.8563 (mtp) cc_final: 0.8094 (mtm) REVERT: R 51 ILE cc_start: 0.7909 (mt) cc_final: 0.7682 (mp) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 1.0535 time to fit residues: 156.2732 Evaluate side-chains 125 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8888 Z= 0.170 Angle : 0.514 10.121 12069 Z= 0.274 Chirality : 0.041 0.163 1377 Planarity : 0.004 0.050 1522 Dihedral : 6.756 91.520 1259 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.10 % Allowed : 27.91 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.04 (0.25), residues: 1115 helix: 1.29 (0.28), residues: 368 sheet: 0.22 (0.32), residues: 255 loop : -1.04 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 188 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE A 354 TYR 0.019 0.001 TYR S 235 ARG 0.007 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.897 Fit side-chains REVERT: A 29 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8169 (ttmt) REVERT: A 272 ASP cc_start: 0.7767 (t0) cc_final: 0.6599 (t0) REVERT: A 276 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: A 349 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7685 (mmmm) REVERT: R 167 MET cc_start: 0.5781 (tpp) cc_final: 0.5552 (tpp) outliers start: 28 outliers final: 10 residues processed: 148 average time/residue: 1.0041 time to fit residues: 160.5548 Evaluate side-chains 135 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 225 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 80 optimal weight: 2.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 82 GLN S 113 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8888 Z= 0.161 Angle : 0.487 7.200 12069 Z= 0.258 Chirality : 0.040 0.158 1377 Planarity : 0.004 0.046 1522 Dihedral : 5.178 40.892 1259 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.10 % Allowed : 27.46 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1115 helix: 1.53 (0.28), residues: 368 sheet: 0.14 (0.32), residues: 261 loop : -0.98 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 188 HIS 0.004 0.001 HIS R 189 PHE 0.023 0.001 PHE R 38 TYR 0.016 0.001 TYR S 235 ARG 0.007 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 0.906 Fit side-chains REVERT: C 47 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: R 167 MET cc_start: 0.5805 (tpp) cc_final: 0.5511 (tpp) outliers start: 37 outliers final: 12 residues processed: 144 average time/residue: 0.9245 time to fit residues: 144.5893 Evaluate side-chains 131 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 59 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 82 GLN S 113 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8888 Z= 0.158 Angle : 0.487 9.877 12069 Z= 0.254 Chirality : 0.040 0.211 1377 Planarity : 0.004 0.047 1522 Dihedral : 4.873 39.902 1259 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.43 % Allowed : 27.91 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1115 helix: 1.63 (0.28), residues: 368 sheet: 0.05 (0.31), residues: 263 loop : -0.96 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 188 HIS 0.005 0.001 HIS R 189 PHE 0.018 0.001 PHE R 38 TYR 0.015 0.001 TYR S 235 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 1.040 Fit side-chains REVERT: A 20 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: A 248 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7840 (ttpp) REVERT: A 272 ASP cc_start: 0.7644 (t0) cc_final: 0.6976 (t0) REVERT: A 276 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: A 349 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7647 (mmmm) REVERT: S 140 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.6780 (mpp) REVERT: S 165 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6071 (pp) REVERT: R 167 MET cc_start: 0.5899 (tpp) cc_final: 0.5612 (tpp) outliers start: 40 outliers final: 21 residues processed: 151 average time/residue: 0.9069 time to fit residues: 148.7675 Evaluate side-chains 149 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 84 MET Chi-restraints excluded: chain R residue 189 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8888 Z= 0.299 Angle : 0.564 7.891 12069 Z= 0.295 Chirality : 0.043 0.243 1377 Planarity : 0.004 0.046 1522 Dihedral : 5.426 43.981 1259 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 6.09 % Allowed : 27.24 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1115 helix: 1.48 (0.28), residues: 366 sheet: 0.04 (0.31), residues: 255 loop : -1.00 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 188 HIS 0.005 0.001 HIS R 189 PHE 0.023 0.002 PHE R 232 TYR 0.019 0.001 TYR S 235 ARG 0.006 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 129 time to evaluate : 1.032 Fit side-chains REVERT: A 20 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: A 244 HIS cc_start: 0.8195 (m90) cc_final: 0.7768 (m90) REVERT: A 272 ASP cc_start: 0.7778 (t0) cc_final: 0.7028 (t0) REVERT: A 276 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: S 165 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.5994 (pp) REVERT: S 235 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6754 (t80) REVERT: B 42 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7596 (ttm-80) REVERT: R 25 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.6579 (m-10) outliers start: 55 outliers final: 27 residues processed: 167 average time/residue: 0.9225 time to fit residues: 167.3315 Evaluate side-chains 156 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 84 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 189 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 82 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8888 Z= 0.177 Angle : 0.513 8.976 12069 Z= 0.266 Chirality : 0.041 0.245 1377 Planarity : 0.004 0.047 1522 Dihedral : 5.187 41.691 1259 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.09 % Allowed : 28.68 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1115 helix: 1.63 (0.28), residues: 363 sheet: -0.03 (0.31), residues: 261 loop : -0.99 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 188 HIS 0.006 0.001 HIS R 189 PHE 0.013 0.001 PHE R 38 TYR 0.018 0.001 TYR S 235 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 125 time to evaluate : 0.920 Fit side-chains REVERT: A 20 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: A 272 ASP cc_start: 0.7724 (t0) cc_final: 0.7133 (t0) REVERT: A 276 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: A 349 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7626 (mmmm) REVERT: S 165 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.5996 (pp) REVERT: S 235 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6643 (t80) REVERT: B 42 ARG cc_start: 0.7781 (tpt170) cc_final: 0.7553 (ttm-80) REVERT: R 167 MET cc_start: 0.6051 (mmm) cc_final: 0.5731 (tpp) outliers start: 46 outliers final: 27 residues processed: 157 average time/residue: 0.8934 time to fit residues: 153.0874 Evaluate side-chains 151 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 84 MET Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 242 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 0.3980 chunk 106 optimal weight: 0.1980 chunk 66 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.0270 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8888 Z= 0.133 Angle : 0.476 8.233 12069 Z= 0.248 Chirality : 0.040 0.152 1377 Planarity : 0.004 0.049 1522 Dihedral : 4.738 38.096 1259 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.21 % Allowed : 30.56 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1115 helix: 1.97 (0.28), residues: 357 sheet: 0.04 (0.31), residues: 268 loop : -0.97 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 188 HIS 0.006 0.000 HIS R 189 PHE 0.013 0.001 PHE R 38 TYR 0.014 0.001 TYR S 235 ARG 0.004 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 0.981 Fit side-chains REVERT: A 20 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: A 248 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7830 (ttpp) REVERT: A 272 ASP cc_start: 0.7663 (t0) cc_final: 0.7181 (t0) REVERT: A 276 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: A 349 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7615 (mmmm) REVERT: S 165 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.5901 (pp) REVERT: S 235 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.6403 (t80) REVERT: R 167 MET cc_start: 0.6052 (mmm) cc_final: 0.5720 (tpp) outliers start: 29 outliers final: 13 residues processed: 149 average time/residue: 0.9124 time to fit residues: 147.9110 Evaluate side-chains 140 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 189 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 0.0050 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 82 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8888 Z= 0.162 Angle : 0.495 9.033 12069 Z= 0.258 Chirality : 0.041 0.250 1377 Planarity : 0.004 0.048 1522 Dihedral : 4.725 36.765 1257 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.21 % Allowed : 30.90 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1115 helix: 1.90 (0.28), residues: 360 sheet: 0.08 (0.31), residues: 268 loop : -0.93 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 188 HIS 0.005 0.001 HIS R 189 PHE 0.012 0.001 PHE A 354 TYR 0.014 0.001 TYR S 235 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 1.006 Fit side-chains REVERT: A 20 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: A 248 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7850 (ttpp) REVERT: A 349 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7635 (mmmm) REVERT: S 22 CYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7539 (t) REVERT: S 165 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.5946 (pp) REVERT: S 235 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6468 (t80) REVERT: R 167 MET cc_start: 0.6201 (mmm) cc_final: 0.5830 (tpp) outliers start: 29 outliers final: 16 residues processed: 146 average time/residue: 0.9071 time to fit residues: 144.1442 Evaluate side-chains 139 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 189 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8888 Z= 0.230 Angle : 0.538 9.345 12069 Z= 0.280 Chirality : 0.042 0.253 1377 Planarity : 0.004 0.047 1522 Dihedral : 5.059 37.763 1257 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.54 % Allowed : 31.34 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1115 helix: 1.65 (0.28), residues: 366 sheet: 0.08 (0.31), residues: 261 loop : -1.00 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 188 HIS 0.005 0.001 HIS R 189 PHE 0.024 0.001 PHE R 232 TYR 0.016 0.001 TYR S 235 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 0.958 Fit side-chains REVERT: A 20 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: A 272 ASP cc_start: 0.7702 (t0) cc_final: 0.7173 (t0) REVERT: A 276 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: A 349 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7674 (mmmm) REVERT: S 22 CYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7531 (t) REVERT: S 165 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.5963 (pp) REVERT: S 235 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6664 (t80) REVERT: B 42 ARG cc_start: 0.7767 (tpt170) cc_final: 0.7533 (ttm-80) REVERT: R 101 ARG cc_start: 0.7166 (ttm-80) cc_final: 0.6788 (mtp180) outliers start: 32 outliers final: 21 residues processed: 146 average time/residue: 0.9314 time to fit residues: 147.6900 Evaluate side-chains 145 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 189 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8888 Z= 0.163 Angle : 0.514 9.923 12069 Z= 0.267 Chirality : 0.041 0.265 1377 Planarity : 0.004 0.047 1522 Dihedral : 4.842 35.683 1257 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.99 % Allowed : 31.89 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1115 helix: 1.87 (0.28), residues: 358 sheet: 0.09 (0.31), residues: 266 loop : -0.99 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 188 HIS 0.006 0.001 HIS R 189 PHE 0.012 0.001 PHE A 354 TYR 0.016 0.001 TYR S 235 ARG 0.004 0.000 ARG S 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.044 Fit side-chains REVERT: A 20 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: A 248 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7877 (ttpp) REVERT: A 349 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7639 (mmmm) REVERT: S 22 CYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7459 (t) REVERT: S 165 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.5947 (pp) REVERT: S 235 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6416 (t80) REVERT: R 258 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7048 (tp) outliers start: 27 outliers final: 19 residues processed: 145 average time/residue: 0.9359 time to fit residues: 147.3856 Evaluate side-chains 144 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.171191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132683 restraints weight = 9951.165| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.01 r_work: 0.3400 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8888 Z= 0.209 Angle : 0.548 9.874 12069 Z= 0.282 Chirality : 0.042 0.266 1377 Planarity : 0.004 0.048 1522 Dihedral : 4.937 35.460 1257 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.21 % Allowed : 32.00 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1115 helix: 1.83 (0.28), residues: 358 sheet: 0.03 (0.31), residues: 266 loop : -1.03 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 188 HIS 0.005 0.001 HIS R 189 PHE 0.015 0.001 PHE R 232 TYR 0.016 0.001 TYR S 235 ARG 0.005 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3459.97 seconds wall clock time: 62 minutes 21.62 seconds (3741.62 seconds total)