Starting phenix.real_space_refine on Fri Jan 19 18:57:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/01_2024/8hpn_34934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/01_2024/8hpn_34934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/01_2024/8hpn_34934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/01_2024/8hpn_34934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/01_2024/8hpn_34934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpn_34934/01_2024/8hpn_34934_updated.pdb" } resolution = 4.55 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= 0.009 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 P 6 5.49 5 S 23 5.16 5 C 7862 2.51 5 N 2078 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 311": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 361": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 390": "NH1" <-> "NH2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 175": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 368": "NH1" <-> "NH2" Residue "E ARG 409": "NH1" <-> "NH2" Residue "E ARG 445": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12329 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2009 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 14, 'TRANS': 269} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1904 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 248} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2563 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain breaks: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 116 Chain: "D" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2577 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 103 Chain: "E" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3191 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 31, 'TRANS': 404} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 90 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.18, per 1000 atoms: 0.58 Number of scatterers: 12329 At special positions: 0 Unit cell: (81.18, 89.38, 167.28, 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 23 16.00 P 6 15.00 O 2360 8.00 N 2078 7.00 C 7862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-1 " GLC G 1 " - " GLC G 2 " Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 2.4 seconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 15 sheets defined 49.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 18 through 37 Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 77 through 110 removed outlier: 3.771A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.587A pdb=" N ILE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 147 through 150 No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 190 removed outlier: 4.855A pdb=" N TRP A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 207 through 218 Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 224 through 235 removed outlier: 4.424A pdb=" N LEU A 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.537A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 removed outlier: 4.087A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 36 Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 65 through 96 removed outlier: 4.063A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 removed outlier: 4.453A pdb=" N LEU B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 127 removed outlier: 4.185A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 138 through 162 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 181 through 207 Proline residue: B 189 - end of helix Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 242 through 269 Proline residue: B 255 - end of helix removed outlier: 3.736A pdb=" N ILE B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARG B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE B 267 " --> pdb=" O PHE B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 54 removed outlier: 3.668A pdb=" N ASN C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 97 through 107 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 112 through 125 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.640A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 171 through 187 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 267 through 275 removed outlier: 4.013A pdb=" N LEU C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 77 through 80 No H-bonds generated for 'chain 'D' and resid 77 through 80' Processing helix chain 'D' and resid 97 through 107 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 141 through 155 removed outlier: 5.456A pdb=" N ARG D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 171 through 188 Processing helix chain 'D' and resid 199 through 205 removed outlier: 4.023A pdb=" N THR D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 288 through 290 No H-bonds generated for 'chain 'D' and resid 288 through 290' Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'E' and resid 38 through 55 removed outlier: 6.179A pdb=" N ALA E 42 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR E 43 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU E 53 " --> pdb=" O ARG E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 Processing helix chain 'E' and resid 99 through 103 Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 117 through 120 Processing helix chain 'E' and resid 128 through 134 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 242 removed outlier: 4.764A pdb=" N ALA E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 274 through 286 Proline residue: E 278 - end of helix removed outlier: 3.640A pdb=" N GLU E 282 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 314 through 327 Processing helix chain 'E' and resid 361 through 371 Processing helix chain 'E' and resid 373 through 381 removed outlier: 4.044A pdb=" N TYR E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 396 through 400 Processing helix chain 'E' and resid 403 through 414 removed outlier: 3.647A pdb=" N GLN E 410 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR E 413 " --> pdb=" O GLN E 410 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN E 414 " --> pdb=" O GLN E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 435 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 443 through 458 removed outlier: 3.646A pdb=" N ALA E 447 " --> pdb=" O PRO E 443 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 29 through 31 Processing sheet with id= B, first strand: chain 'C' and resid 216 through 221 removed outlier: 6.704A pdb=" N VAL C 211 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE C 220 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 209 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR C 192 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU C 39 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR C 194 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP C 163 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 261 through 264 removed outlier: 3.581A pdb=" N GLY C 261 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 291 through 293 removed outlier: 4.044A pdb=" N GLU C 366 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 314 through 317 Processing sheet with id= F, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.858A pdb=" N TYR C 13 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA C 22 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 29 through 31 Processing sheet with id= H, first strand: chain 'D' and resid 216 through 221 removed outlier: 6.841A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR D 192 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU D 39 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR D 194 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLY D 41 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR D 196 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ASP D 163 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL D 85 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 245 through 249 Processing sheet with id= J, first strand: chain 'D' and resid 255 through 258 removed outlier: 3.667A pdb=" N GLY D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 291 through 293 Processing sheet with id= L, first strand: chain 'D' and resid 314 through 317 Processing sheet with id= M, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.127A pdb=" N TYR D 13 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA D 22 " --> pdb=" O TYR D 13 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 60 through 66 removed outlier: 7.727A pdb=" N TYR E 35 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N MET E 91 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N LEU E 93 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU E 351 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 269 through 272 599 hydrogen bonds defined for protein. 1605 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: 3.39 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2097 1.29 - 1.42: 3083 1.42 - 1.55: 7337 1.55 - 1.68: 20 1.68 - 1.82: 42 Bond restraints: 12579 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.85e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.79e+01 bond pdb=" C LEU A 262 " pdb=" O LEU A 262 " ideal model delta sigma weight residual 1.234 1.173 0.062 8.30e-03 1.45e+04 5.52e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.36e+01 ... (remaining 12574 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.74: 575 106.74 - 114.09: 6773 114.09 - 121.44: 6554 121.44 - 128.79: 3289 128.79 - 136.14: 61 Bond angle restraints: 17252 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.31 19.56 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.52 16.31 1.00e+00 1.00e+00 2.66e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.53 16.30 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.63 8.17 1.00e+00 1.00e+00 6.67e+01 ... (remaining 17247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6897 17.98 - 35.96: 485 35.96 - 53.95: 79 53.95 - 71.93: 29 71.93 - 89.91: 5 Dihedral angle restraints: 7495 sinusoidal: 2581 harmonic: 4914 Sorted by residual: dihedral pdb=" CA ASP E 121 " pdb=" C ASP E 121 " pdb=" N ALA E 122 " pdb=" CA ALA E 122 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA TRP E 106 " pdb=" C TRP E 106 " pdb=" N ALA E 107 " pdb=" CA ALA E 107 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ARG D 134 " pdb=" C ARG D 134 " pdb=" N LYS D 135 " pdb=" CA LYS D 135 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 7492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.924: 2082 0.924 - 1.848: 0 1.848 - 2.773: 0 2.773 - 3.697: 0 3.697 - 4.621: 1 Chirality restraints: 2083 Sorted by residual: chirality pdb=" C1 GLC G 2 " pdb=" C2 GLC G 2 " pdb=" O1 GLC G 2 " pdb=" O5 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.33 -2.29 4.62 2.00e-01 2.50e+01 5.34e+02 chirality pdb=" C1 GLC G 1 " pdb=" C2 GLC G 1 " pdb=" O5 GLC G 1 " pdb=" O1 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.92e+01 chirality pdb=" CA LEU A 262 " pdb=" N LEU A 262 " pdb=" C LEU A 262 " pdb=" CB LEU A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 2080 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 402 " -0.120 2.00e-02 2.50e+03 6.83e-02 9.33e+01 pdb=" CG TYR E 402 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 402 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 402 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR E 402 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR E 402 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR E 402 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 402 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 166 " 0.128 2.00e-02 2.50e+03 5.95e-02 8.85e+01 pdb=" CG TRP E 166 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 166 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP E 166 " -0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP E 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP E 166 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 166 " -0.060 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 166 " 0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 166 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP E 166 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 234 " -0.113 2.00e-02 2.50e+03 6.91e-02 8.35e+01 pdb=" CG PHE C 234 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE C 234 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 PHE C 234 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE C 234 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 234 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE C 234 " -0.063 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1289 2.77 - 3.31: 14768 3.31 - 3.84: 21240 3.84 - 4.37: 24848 4.37 - 4.90: 39198 Nonbonded interactions: 101343 Sorted by model distance: nonbonded pdb=" OD2 ASP B 175 " pdb=" OH TYR C 92 " model vdw 2.243 2.440 nonbonded pdb=" OE1 GLN E 150 " pdb=" CE2 TYR E 333 " model vdw 2.302 3.340 nonbonded pdb=" O ASP E 440 " pdb=" OD1 ASP E 440 " model vdw 2.349 3.040 nonbonded pdb=" CD2 LEU A 185 " pdb=" CD1 ILE A 223 " model vdw 2.408 3.880 nonbonded pdb=" O ILE B 132 " pdb=" N LEU B 134 " model vdw 2.424 2.520 ... (remaining 101338 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 'C' and (resid 2 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 124 or (resid 125 through 128 and ( \ name N or name CA or name C or name O or name CB )) or resid 129 through 142 or \ (resid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 \ through 152 or (resid 153 and (name N or name CA or name C or name O or name CB \ )) or resid 154 through 193 or (resid 194 and (name N or name CA or name C or n \ ame O or name CB )) or resid 195 through 204 or (resid 205 and (name N or name C \ A or name C or name O or name CB )) or resid 206 through 261 or (resid 262 and ( \ name N or name CA or name C or name O or name CB )) or resid 263 through 286 or \ (resid 287 and (name N or name CA or name C or name O or name CB )) or resid 288 \ through 313 or (resid 314 and (name N or name CA or name C or name O or name CB \ )) or resid 315 through 376 or (resid 377 and (name N or name CA or name C or n \ ame O or name CB )) or resid 378 through 385 or (resid 386 and (name N or name C \ A or name C or name O or name CB )) or resid 387 or (resid 388 and (name N or na \ me CA or name C or name O or name CB )) or resid 389 through 391 or resid 501)) selection = (chain 'D' and (resid 2 through 50 or (resid 51 through 52 and (name N or name C \ A or name C or name O or name CB )) or resid 53 through 57 or (resid 58 and (nam \ e N or name CA or name C or name O or name CB )) or resid 59 through 77 or (resi \ d 78 and (name N or name CA or name C or name O or name CB )) or resid 79 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 through 117 or (resid 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 126 or (resid 127 through 128 and (name N or name \ CA or name C or name O or name CB )) or resid 129 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 174 o \ r (resid 175 through 179 and (name N or name CA or name C or name O or name CB ) \ ) or resid 180 through 195 or (resid 196 and (name N or name CA or name C or nam \ e O or name CB )) or resid 197 through 285 or (resid 286 through 287 and (name N \ or name CA or name C or name O or name CB )) or resid 288 through 289 or (resid \ 290 and (name N or name CA or name C or name O or name CB )) or resid 291 throu \ gh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 378 or (resid 379 and (name N or name CA or name C or name O \ or name CB )) or resid 380 or (resid 381 through 383 and (name N or name CA or n \ ame C or name O or name CB )) or resid 384 through 391 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.020 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.910 Find NCS groups from input model: 0.530 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.012 0.139 12579 Z= 0.808 Angle : 1.810 19.565 17252 Z= 1.223 Chirality : 0.141 4.621 2083 Planarity : 0.013 0.105 2235 Dihedral : 13.652 89.910 4319 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.28 % Favored : 92.48 % Rotamer: Outliers : 0.35 % Allowed : 6.92 % Favored : 92.73 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.18), residues: 1689 helix: -1.78 (0.14), residues: 859 sheet: -1.41 (0.39), residues: 126 loop : -1.56 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.128 0.017 TRP E 166 HIS 0.011 0.003 HIS D 290 PHE 0.113 0.017 PHE C 234 TYR 0.120 0.021 TYR E 402 ARG 0.014 0.001 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 310 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9486 (m-80) cc_final: 0.8927 (m-80) REVERT: A 162 GLN cc_start: 0.9526 (tt0) cc_final: 0.9069 (tp40) REVERT: A 166 LEU cc_start: 0.9803 (mt) cc_final: 0.9551 (mt) REVERT: A 176 LYS cc_start: 0.9433 (tptp) cc_final: 0.9090 (tppt) REVERT: A 233 ASP cc_start: 0.8725 (m-30) cc_final: 0.8246 (m-30) REVERT: A 260 ASP cc_start: 0.9013 (t0) cc_final: 0.8443 (t0) REVERT: A 261 ASN cc_start: 0.9085 (m-40) cc_final: 0.8870 (m-40) REVERT: A 289 TYR cc_start: 0.9466 (m-80) cc_final: 0.9217 (m-10) REVERT: A 291 LYS cc_start: 0.8916 (tptt) cc_final: 0.8671 (mmtp) REVERT: B 113 ILE cc_start: 0.9423 (pt) cc_final: 0.9186 (mm) REVERT: B 116 PHE cc_start: 0.8800 (m-80) cc_final: 0.8216 (m-80) REVERT: B 127 ASN cc_start: 0.9537 (m-40) cc_final: 0.9106 (m110) REVERT: B 144 PRO cc_start: 0.9529 (Cg_exo) cc_final: 0.9253 (Cg_endo) REVERT: B 148 PHE cc_start: 0.9528 (m-80) cc_final: 0.9290 (m-80) REVERT: B 174 MET cc_start: 0.9284 (mtp) cc_final: 0.9063 (ttt) REVERT: C 163 ASP cc_start: 0.8276 (m-30) cc_final: 0.7966 (t0) REVERT: C 239 ILE cc_start: 0.8991 (tp) cc_final: 0.8666 (pt) REVERT: D 177 MET cc_start: 0.9143 (mmm) cc_final: 0.8689 (mmp) REVERT: D 269 MET cc_start: 0.8702 (mtt) cc_final: 0.8221 (mmm) REVERT: E 91 MET cc_start: 0.8946 (ptp) cc_final: 0.8689 (ptp) REVERT: E 153 TRP cc_start: 0.8691 (m100) cc_final: 0.8438 (m100) REVERT: E 154 TYR cc_start: 0.8947 (p90) cc_final: 0.8233 (p90) outliers start: 4 outliers final: 0 residues processed: 313 average time/residue: 0.2516 time to fit residues: 110.0830 Evaluate side-chains 203 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 chunk 98 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS C 99 GLN C 164 GLN D 99 GLN ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 174 ASN E 191 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12579 Z= 0.234 Angle : 0.752 10.049 17252 Z= 0.397 Chirality : 0.047 0.231 2083 Planarity : 0.006 0.057 2235 Dihedral : 8.206 72.799 1881 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 0.35 % Allowed : 4.33 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1689 helix: -0.29 (0.17), residues: 852 sheet: -1.10 (0.35), residues: 157 loop : -1.03 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 97 HIS 0.006 0.001 HIS C 94 PHE 0.029 0.002 PHE E 310 TYR 0.022 0.002 TYR A 41 ARG 0.011 0.001 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 260 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9489 (m-80) cc_final: 0.9022 (m-80) REVERT: A 150 ASN cc_start: 0.8593 (t0) cc_final: 0.8222 (m-40) REVERT: A 161 ASP cc_start: 0.9362 (m-30) cc_final: 0.9143 (m-30) REVERT: A 162 GLN cc_start: 0.9631 (tt0) cc_final: 0.8901 (tp40) REVERT: A 166 LEU cc_start: 0.9820 (mt) cc_final: 0.9604 (mt) REVERT: A 176 LYS cc_start: 0.9463 (tptp) cc_final: 0.9144 (tppt) REVERT: A 227 LEU cc_start: 0.9214 (tt) cc_final: 0.8989 (tt) REVERT: A 229 PHE cc_start: 0.8861 (t80) cc_final: 0.8537 (t80) REVERT: A 260 ASP cc_start: 0.9127 (t0) cc_final: 0.8574 (t0) REVERT: A 261 ASN cc_start: 0.9288 (m-40) cc_final: 0.9044 (m-40) REVERT: A 263 PHE cc_start: 0.9444 (m-80) cc_final: 0.9177 (m-80) REVERT: B 90 MET cc_start: 0.8260 (mmp) cc_final: 0.7658 (tmm) REVERT: B 116 PHE cc_start: 0.8790 (m-80) cc_final: 0.8566 (m-80) REVERT: B 118 HIS cc_start: 0.9164 (m-70) cc_final: 0.8599 (m-70) REVERT: B 127 ASN cc_start: 0.9536 (m-40) cc_final: 0.9012 (m110) REVERT: B 162 ARG cc_start: 0.9187 (mtp180) cc_final: 0.8987 (mtp180) REVERT: B 168 LEU cc_start: 0.9504 (pt) cc_final: 0.9247 (mm) REVERT: B 170 LYS cc_start: 0.9619 (mmtm) cc_final: 0.9403 (mmtt) REVERT: B 203 PHE cc_start: 0.9505 (t80) cc_final: 0.9272 (t80) REVERT: C 163 ASP cc_start: 0.8822 (m-30) cc_final: 0.8280 (t0) REVERT: C 239 ILE cc_start: 0.9118 (tp) cc_final: 0.8702 (pt) REVERT: C 244 MET cc_start: 0.8538 (tpp) cc_final: 0.8081 (tpt) REVERT: E 166 TRP cc_start: 0.8583 (m100) cc_final: 0.8333 (m100) REVERT: E 262 LEU cc_start: 0.9590 (tp) cc_final: 0.9363 (tp) outliers start: 4 outliers final: 0 residues processed: 261 average time/residue: 0.2148 time to fit residues: 82.4908 Evaluate side-chains 192 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 52 optimal weight: 0.0370 chunk 123 optimal weight: 0.0270 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12579 Z= 0.175 Angle : 0.667 8.628 17252 Z= 0.343 Chirality : 0.044 0.199 2083 Planarity : 0.005 0.054 2235 Dihedral : 7.235 73.663 1881 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.26 % Favored : 95.62 % Rotamer: Outliers : 0.17 % Allowed : 3.37 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.53 (0.20), residues: 1689 helix: 0.24 (0.18), residues: 848 sheet: -0.54 (0.35), residues: 165 loop : -0.95 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 97 HIS 0.005 0.001 HIS C 94 PHE 0.022 0.001 PHE E 310 TYR 0.015 0.002 TYR B 57 ARG 0.007 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 255 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8845 (t80) cc_final: 0.8578 (t80) REVERT: A 139 TYR cc_start: 0.9493 (m-80) cc_final: 0.8974 (m-80) REVERT: A 150 ASN cc_start: 0.8647 (t0) cc_final: 0.8313 (m-40) REVERT: A 161 ASP cc_start: 0.9328 (m-30) cc_final: 0.8969 (m-30) REVERT: A 162 GLN cc_start: 0.9604 (tt0) cc_final: 0.8638 (tp40) REVERT: A 176 LYS cc_start: 0.9467 (tptp) cc_final: 0.9186 (tppt) REVERT: A 227 LEU cc_start: 0.9223 (tt) cc_final: 0.8998 (tt) REVERT: A 260 ASP cc_start: 0.9089 (t0) cc_final: 0.8608 (t0) REVERT: A 261 ASN cc_start: 0.9196 (m-40) cc_final: 0.8954 (m-40) REVERT: B 90 MET cc_start: 0.8106 (mmp) cc_final: 0.7671 (tmm) REVERT: B 93 TYR cc_start: 0.9362 (t80) cc_final: 0.9130 (t80) REVERT: B 113 ILE cc_start: 0.9433 (pt) cc_final: 0.9227 (pt) REVERT: B 118 HIS cc_start: 0.9229 (m-70) cc_final: 0.8930 (m-70) REVERT: B 121 LEU cc_start: 0.9402 (mm) cc_final: 0.8831 (mm) REVERT: B 127 ASN cc_start: 0.9528 (m-40) cc_final: 0.8848 (m110) REVERT: B 128 MET cc_start: 0.9371 (mmt) cc_final: 0.8800 (mmm) REVERT: B 145 TYR cc_start: 0.9148 (m-10) cc_final: 0.8520 (m-80) REVERT: B 168 LEU cc_start: 0.9505 (pt) cc_final: 0.9263 (mm) REVERT: B 207 TRP cc_start: 0.8731 (t60) cc_final: 0.8522 (t60) REVERT: C 162 MET cc_start: 0.9314 (mpp) cc_final: 0.9057 (mpp) REVERT: C 163 ASP cc_start: 0.8724 (m-30) cc_final: 0.8052 (t0) REVERT: C 244 MET cc_start: 0.8505 (tpp) cc_final: 0.7965 (tpt) REVERT: D 212 MET cc_start: 0.6055 (tpt) cc_final: 0.5333 (tpt) REVERT: E 40 GLU cc_start: 0.9224 (tt0) cc_final: 0.8808 (tt0) REVERT: E 79 ARG cc_start: 0.8827 (ttt-90) cc_final: 0.8610 (ttt-90) REVERT: E 91 MET cc_start: 0.8928 (ptp) cc_final: 0.8651 (pmm) outliers start: 2 outliers final: 0 residues processed: 255 average time/residue: 0.2244 time to fit residues: 84.8862 Evaluate side-chains 192 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12579 Z= 0.173 Angle : 0.629 13.646 17252 Z= 0.322 Chirality : 0.043 0.189 2083 Planarity : 0.005 0.071 2235 Dihedral : 6.939 76.288 1881 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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 (0.21), residues: 1689 helix: 0.46 (0.18), residues: 848 sheet: -0.78 (0.34), residues: 180 loop : -0.84 (0.26), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 136 HIS 0.004 0.001 HIS C 94 PHE 0.020 0.001 PHE A 263 TYR 0.015 0.002 TYR E 333 ARG 0.004 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8706 (tm-30) REVERT: A 139 TYR cc_start: 0.9498 (m-80) cc_final: 0.9081 (m-80) REVERT: A 150 ASN cc_start: 0.8649 (t0) cc_final: 0.8276 (m-40) REVERT: A 161 ASP cc_start: 0.9115 (m-30) cc_final: 0.8855 (m-30) REVERT: A 162 GLN cc_start: 0.9535 (tt0) cc_final: 0.8958 (tp-100) REVERT: A 176 LYS cc_start: 0.9465 (tptp) cc_final: 0.9177 (tppt) REVERT: A 227 LEU cc_start: 0.9210 (tt) cc_final: 0.8931 (tt) REVERT: A 229 PHE cc_start: 0.9004 (t80) cc_final: 0.8666 (t80) REVERT: A 260 ASP cc_start: 0.9051 (t0) cc_final: 0.8608 (t0) REVERT: A 261 ASN cc_start: 0.9262 (m-40) cc_final: 0.8969 (m-40) REVERT: B 32 LEU cc_start: 0.9614 (mm) cc_final: 0.9282 (mm) REVERT: B 36 LEU cc_start: 0.9586 (mm) cc_final: 0.8887 (mm) REVERT: B 57 TYR cc_start: 0.9038 (m-80) cc_final: 0.8825 (m-80) REVERT: B 58 LYS cc_start: 0.9785 (ptpp) cc_final: 0.9452 (mmtt) REVERT: B 90 MET cc_start: 0.8059 (mmp) cc_final: 0.7641 (tmm) REVERT: B 93 TYR cc_start: 0.9375 (t80) cc_final: 0.9159 (t80) REVERT: B 116 PHE cc_start: 0.7842 (t80) cc_final: 0.7389 (t80) REVERT: B 118 HIS cc_start: 0.9174 (m-70) cc_final: 0.8831 (m-70) REVERT: B 121 LEU cc_start: 0.9521 (mm) cc_final: 0.9246 (mm) REVERT: B 127 ASN cc_start: 0.9529 (m-40) cc_final: 0.8959 (m110) REVERT: B 145 TYR cc_start: 0.9150 (m-10) cc_final: 0.8510 (m-80) REVERT: B 168 LEU cc_start: 0.9480 (pt) cc_final: 0.9238 (mm) REVERT: B 174 MET cc_start: 0.8963 (ttt) cc_final: 0.8713 (mmt) REVERT: B 203 PHE cc_start: 0.9259 (t80) cc_final: 0.9025 (t80) REVERT: B 238 PHE cc_start: 0.8906 (m-80) cc_final: 0.8592 (m-80) REVERT: C 162 MET cc_start: 0.9302 (mpp) cc_final: 0.8955 (mpp) REVERT: C 163 ASP cc_start: 0.8758 (m-30) cc_final: 0.8058 (t0) REVERT: C 244 MET cc_start: 0.8540 (tpp) cc_final: 0.8093 (tpt) REVERT: D 86 PHE cc_start: 0.9403 (t80) cc_final: 0.9147 (t80) REVERT: D 212 MET cc_start: 0.6139 (tpt) cc_final: 0.5537 (tpt) REVERT: E 40 GLU cc_start: 0.9091 (tt0) cc_final: 0.8875 (tt0) REVERT: E 91 MET cc_start: 0.8958 (ptp) cc_final: 0.8692 (pmm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2087 time to fit residues: 77.7426 Evaluate side-chains 190 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 41 optimal weight: 0.0570 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12579 Z= 0.196 Angle : 0.626 7.119 17252 Z= 0.322 Chirality : 0.043 0.190 2083 Planarity : 0.005 0.049 2235 Dihedral : 6.898 77.953 1881 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.19 (0.21), residues: 1689 helix: 0.66 (0.18), residues: 846 sheet: -0.70 (0.33), residues: 187 loop : -0.89 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 207 HIS 0.003 0.001 HIS C 94 PHE 0.018 0.002 PHE A 263 TYR 0.018 0.002 TYR E 333 ARG 0.005 0.000 ARG E 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9496 (m-80) cc_final: 0.9070 (m-80) REVERT: A 150 ASN cc_start: 0.8719 (t0) cc_final: 0.8341 (m-40) REVERT: A 162 GLN cc_start: 0.9568 (tt0) cc_final: 0.8967 (tp40) REVERT: A 176 LYS cc_start: 0.9480 (tptp) cc_final: 0.9161 (tppt) REVERT: A 227 LEU cc_start: 0.9283 (tt) cc_final: 0.9001 (tt) REVERT: A 229 PHE cc_start: 0.9069 (t80) cc_final: 0.8809 (t80) REVERT: A 260 ASP cc_start: 0.9124 (t0) cc_final: 0.8758 (t0) REVERT: A 261 ASN cc_start: 0.9268 (m-40) cc_final: 0.9041 (m-40) REVERT: A 291 LYS cc_start: 0.9122 (tptt) cc_final: 0.8921 (pttm) REVERT: B 32 LEU cc_start: 0.9635 (mm) cc_final: 0.9426 (mm) REVERT: B 58 LYS cc_start: 0.9767 (ptpp) cc_final: 0.9451 (mmtt) REVERT: B 90 MET cc_start: 0.8140 (mmp) cc_final: 0.7662 (tmm) REVERT: B 93 TYR cc_start: 0.9358 (t80) cc_final: 0.9109 (t80) REVERT: B 118 HIS cc_start: 0.9136 (m-70) cc_final: 0.8618 (m-70) REVERT: B 127 ASN cc_start: 0.9519 (m-40) cc_final: 0.9095 (m110) REVERT: B 174 MET cc_start: 0.9086 (ttt) cc_final: 0.8851 (mmt) REVERT: B 203 PHE cc_start: 0.9285 (t80) cc_final: 0.8985 (t80) REVERT: B 238 PHE cc_start: 0.8953 (m-80) cc_final: 0.8717 (m-80) REVERT: C 162 MET cc_start: 0.9318 (mpp) cc_final: 0.9009 (mpp) REVERT: C 163 ASP cc_start: 0.8894 (m-30) cc_final: 0.8160 (t0) REVERT: D 177 MET cc_start: 0.9022 (mmp) cc_final: 0.8613 (mmp) REVERT: D 212 MET cc_start: 0.6369 (tpt) cc_final: 0.5760 (tpt) REVERT: D 224 ASP cc_start: 0.9568 (t0) cc_final: 0.9172 (p0) REVERT: E 44 PHE cc_start: 0.9225 (m-80) cc_final: 0.8798 (m-80) REVERT: E 101 PHE cc_start: 0.9276 (m-80) cc_final: 0.9050 (m-80) REVERT: E 159 MET cc_start: 0.8318 (ppp) cc_final: 0.8061 (ppp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2059 time to fit residues: 74.5266 Evaluate side-chains 179 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.0270 chunk 147 optimal weight: 9.9990 chunk 32 optimal weight: 0.0470 chunk 95 optimal weight: 0.1980 chunk 40 optimal weight: 0.0070 chunk 163 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12579 Z= 0.156 Angle : 0.616 7.327 17252 Z= 0.308 Chirality : 0.043 0.208 2083 Planarity : 0.005 0.047 2235 Dihedral : 6.787 74.238 1881 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.26 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.12 (0.21), residues: 1689 helix: 0.76 (0.18), residues: 854 sheet: -0.69 (0.34), residues: 180 loop : -0.93 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 79 HIS 0.003 0.001 HIS C 94 PHE 0.024 0.001 PHE B 116 TYR 0.017 0.001 TYR E 333 ARG 0.004 0.000 ARG E 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8837 (t80) cc_final: 0.8411 (t80) REVERT: A 58 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8772 (tm-30) REVERT: A 139 TYR cc_start: 0.9487 (m-80) cc_final: 0.9169 (m-80) REVERT: A 150 ASN cc_start: 0.8719 (t0) cc_final: 0.8355 (m-40) REVERT: A 162 GLN cc_start: 0.9560 (tt0) cc_final: 0.8990 (tp-100) REVERT: A 176 LYS cc_start: 0.9464 (tptp) cc_final: 0.9167 (tppt) REVERT: A 227 LEU cc_start: 0.9163 (tt) cc_final: 0.8840 (tt) REVERT: A 229 PHE cc_start: 0.9086 (t80) cc_final: 0.8664 (t80) REVERT: A 233 ASP cc_start: 0.8916 (m-30) cc_final: 0.8710 (m-30) REVERT: A 260 ASP cc_start: 0.9102 (t0) cc_final: 0.8711 (t0) REVERT: A 291 LYS cc_start: 0.9126 (tptt) cc_final: 0.8903 (mmtp) REVERT: B 32 LEU cc_start: 0.9606 (mm) cc_final: 0.9293 (mm) REVERT: B 36 LEU cc_start: 0.9580 (mm) cc_final: 0.8784 (mm) REVERT: B 58 LYS cc_start: 0.9734 (ptpp) cc_final: 0.9440 (mmtt) REVERT: B 90 MET cc_start: 0.8097 (mmp) cc_final: 0.7664 (tmm) REVERT: B 118 HIS cc_start: 0.9217 (m-70) cc_final: 0.8729 (m-70) REVERT: B 127 ASN cc_start: 0.9502 (m-40) cc_final: 0.8903 (m110) REVERT: B 128 MET cc_start: 0.9437 (mmt) cc_final: 0.8848 (mmt) REVERT: B 174 MET cc_start: 0.9060 (ttt) cc_final: 0.8855 (mmt) REVERT: B 203 PHE cc_start: 0.9207 (t80) cc_final: 0.8957 (t80) REVERT: B 238 PHE cc_start: 0.8889 (m-80) cc_final: 0.8346 (m-10) REVERT: C 163 ASP cc_start: 0.8779 (m-30) cc_final: 0.7961 (t0) REVERT: C 244 MET cc_start: 0.8591 (tpp) cc_final: 0.8208 (tpt) REVERT: D 212 MET cc_start: 0.6108 (tpt) cc_final: 0.5694 (tpt) REVERT: D 224 ASP cc_start: 0.9504 (t0) cc_final: 0.9115 (p0) REVERT: E 159 MET cc_start: 0.8384 (ppp) cc_final: 0.8105 (ppp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2146 time to fit residues: 81.6278 Evaluate side-chains 188 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 0.0870 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12579 Z= 0.227 Angle : 0.642 8.060 17252 Z= 0.332 Chirality : 0.043 0.210 2083 Planarity : 0.005 0.044 2235 Dihedral : 6.817 77.084 1881 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.27 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.04 (0.21), residues: 1689 helix: 0.84 (0.18), residues: 848 sheet: -0.66 (0.35), residues: 168 loop : -0.89 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 79 HIS 0.006 0.001 HIS D 290 PHE 0.023 0.002 PHE A 279 TYR 0.014 0.002 TYR A 45 ARG 0.014 0.001 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8890 (t80) cc_final: 0.8483 (t80) REVERT: A 139 TYR cc_start: 0.9496 (m-80) cc_final: 0.9067 (m-80) REVERT: A 150 ASN cc_start: 0.8785 (t0) cc_final: 0.8473 (m-40) REVERT: A 162 GLN cc_start: 0.9591 (tt0) cc_final: 0.8990 (tp-100) REVERT: A 176 LYS cc_start: 0.9483 (tptp) cc_final: 0.9123 (tppt) REVERT: A 227 LEU cc_start: 0.9309 (tt) cc_final: 0.8993 (tt) REVERT: A 229 PHE cc_start: 0.9177 (t80) cc_final: 0.8810 (t80) REVERT: A 233 ASP cc_start: 0.8904 (m-30) cc_final: 0.8694 (m-30) REVERT: A 260 ASP cc_start: 0.9155 (t0) cc_final: 0.8853 (t0) REVERT: A 291 LYS cc_start: 0.9215 (tptt) cc_final: 0.9008 (mmtp) REVERT: B 32 LEU cc_start: 0.9623 (mm) cc_final: 0.9327 (mm) REVERT: B 36 LEU cc_start: 0.9596 (mm) cc_final: 0.8739 (mm) REVERT: B 57 TYR cc_start: 0.9253 (m-10) cc_final: 0.9030 (m-80) REVERT: B 58 LYS cc_start: 0.9741 (ptpp) cc_final: 0.9403 (mmtt) REVERT: B 90 MET cc_start: 0.8157 (mmp) cc_final: 0.7739 (tmm) REVERT: B 118 HIS cc_start: 0.9166 (m-70) cc_final: 0.8470 (m-70) REVERT: B 127 ASN cc_start: 0.9530 (m-40) cc_final: 0.8966 (m110) REVERT: B 128 MET cc_start: 0.9576 (mmt) cc_final: 0.9044 (mmm) REVERT: B 203 PHE cc_start: 0.9250 (t80) cc_final: 0.8965 (t80) REVERT: C 163 ASP cc_start: 0.8943 (m-30) cc_final: 0.8510 (p0) REVERT: C 244 MET cc_start: 0.8620 (tpp) cc_final: 0.8259 (tpt) REVERT: D 86 PHE cc_start: 0.9377 (t80) cc_final: 0.9108 (t80) REVERT: D 224 ASP cc_start: 0.9545 (t0) cc_final: 0.9141 (p0) REVERT: E 44 PHE cc_start: 0.9155 (m-80) cc_final: 0.8722 (m-80) REVERT: E 159 MET cc_start: 0.8407 (ppp) cc_final: 0.8093 (ppp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2030 time to fit residues: 72.1549 Evaluate side-chains 176 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 80 optimal weight: 0.0040 chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12579 Z= 0.152 Angle : 0.607 7.172 17252 Z= 0.304 Chirality : 0.043 0.242 2083 Planarity : 0.005 0.044 2235 Dihedral : 6.656 75.484 1881 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 0.08 (0.21), residues: 1689 helix: 0.94 (0.19), residues: 845 sheet: -0.55 (0.36), residues: 168 loop : -0.86 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 79 HIS 0.003 0.001 HIS C 94 PHE 0.016 0.001 PHE C 160 TYR 0.018 0.002 TYR E 402 ARG 0.007 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8844 (t80) cc_final: 0.8415 (t80) REVERT: A 139 TYR cc_start: 0.9496 (m-80) cc_final: 0.9088 (m-80) REVERT: A 150 ASN cc_start: 0.8754 (t0) cc_final: 0.8411 (m-40) REVERT: A 162 GLN cc_start: 0.9572 (tt0) cc_final: 0.8970 (tp-100) REVERT: A 176 LYS cc_start: 0.9470 (tptp) cc_final: 0.9160 (tppt) REVERT: A 227 LEU cc_start: 0.9253 (tt) cc_final: 0.8929 (tt) REVERT: A 229 PHE cc_start: 0.9130 (t80) cc_final: 0.8718 (t80) REVERT: A 233 ASP cc_start: 0.8898 (m-30) cc_final: 0.8653 (m-30) REVERT: A 259 TYR cc_start: 0.9024 (t80) cc_final: 0.8730 (t80) REVERT: A 260 ASP cc_start: 0.9136 (t0) cc_final: 0.8823 (t0) REVERT: A 291 LYS cc_start: 0.9251 (tptt) cc_final: 0.9017 (mmtp) REVERT: B 32 LEU cc_start: 0.9607 (mm) cc_final: 0.9316 (mm) REVERT: B 36 LEU cc_start: 0.9599 (mm) cc_final: 0.8714 (mm) REVERT: B 58 LYS cc_start: 0.9726 (ptpp) cc_final: 0.9402 (mmtt) REVERT: B 90 MET cc_start: 0.8186 (mmp) cc_final: 0.7759 (tmm) REVERT: B 118 HIS cc_start: 0.9234 (m-70) cc_final: 0.8724 (m-70) REVERT: B 127 ASN cc_start: 0.9504 (m-40) cc_final: 0.8915 (m110) REVERT: B 128 MET cc_start: 0.9532 (mmt) cc_final: 0.8984 (mmt) REVERT: B 203 PHE cc_start: 0.9221 (t80) cc_final: 0.8963 (t80) REVERT: C 163 ASP cc_start: 0.8859 (m-30) cc_final: 0.8336 (p0) REVERT: C 216 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8803 (mm-30) REVERT: C 244 MET cc_start: 0.8632 (tpp) cc_final: 0.8302 (tpt) REVERT: D 224 ASP cc_start: 0.9532 (t0) cc_final: 0.9143 (p0) REVERT: E 44 PHE cc_start: 0.9119 (m-80) cc_final: 0.8682 (m-80) REVERT: E 159 MET cc_start: 0.8418 (ppp) cc_final: 0.8051 (ppp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1984 time to fit residues: 72.4531 Evaluate side-chains 184 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 160 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 148 ASN ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12579 Z= 0.236 Angle : 0.646 6.861 17252 Z= 0.332 Chirality : 0.043 0.233 2083 Planarity : 0.005 0.043 2235 Dihedral : 6.795 78.997 1881 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.45 % Favored : 94.43 % Rotamer: Outliers : 0.09 % Allowed : 0.87 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: -0.03 (0.21), residues: 1689 helix: 0.86 (0.18), residues: 845 sheet: -0.47 (0.36), residues: 175 loop : -0.96 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 79 HIS 0.003 0.001 HIS D 290 PHE 0.017 0.002 PHE E 310 TYR 0.018 0.002 TYR E 393 ARG 0.016 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8918 (t80) cc_final: 0.8485 (t80) REVERT: A 137 TRP cc_start: 0.9339 (m100) cc_final: 0.9069 (m100) REVERT: A 139 TYR cc_start: 0.9495 (m-80) cc_final: 0.8966 (m-80) REVERT: A 150 ASN cc_start: 0.8837 (t0) cc_final: 0.8506 (m-40) REVERT: A 162 GLN cc_start: 0.9600 (tt0) cc_final: 0.9034 (tp-100) REVERT: A 176 LYS cc_start: 0.9479 (tptp) cc_final: 0.9105 (tppt) REVERT: A 227 LEU cc_start: 0.9342 (tt) cc_final: 0.9027 (tt) REVERT: A 229 PHE cc_start: 0.9226 (t80) cc_final: 0.8871 (t80) REVERT: A 233 ASP cc_start: 0.8909 (m-30) cc_final: 0.8696 (m-30) REVERT: A 260 ASP cc_start: 0.9211 (t0) cc_final: 0.8925 (t0) REVERT: A 291 LYS cc_start: 0.9307 (tptt) cc_final: 0.9051 (pttm) REVERT: B 32 LEU cc_start: 0.9652 (mm) cc_final: 0.9407 (mm) REVERT: B 90 MET cc_start: 0.8205 (mmp) cc_final: 0.7730 (tmm) REVERT: B 118 HIS cc_start: 0.9206 (m-70) cc_final: 0.8522 (m-70) REVERT: B 127 ASN cc_start: 0.9512 (m-40) cc_final: 0.8931 (m110) REVERT: B 128 MET cc_start: 0.9628 (mmt) cc_final: 0.9137 (mmm) REVERT: C 163 ASP cc_start: 0.8969 (m-30) cc_final: 0.8525 (p0) REVERT: C 244 MET cc_start: 0.8680 (tpp) cc_final: 0.8360 (tpt) REVERT: D 86 PHE cc_start: 0.9388 (t80) cc_final: 0.9154 (t80) REVERT: D 224 ASP cc_start: 0.9562 (t0) cc_final: 0.9135 (p0) REVERT: D 244 MET cc_start: 0.4818 (tpt) cc_final: 0.4483 (tpp) REVERT: E 44 PHE cc_start: 0.9119 (m-80) cc_final: 0.8667 (m-80) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.2031 time to fit residues: 73.6627 Evaluate side-chains 175 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 134 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 12579 Z= 0.184 Angle : 0.613 7.174 17252 Z= 0.310 Chirality : 0.043 0.259 2083 Planarity : 0.005 0.046 2235 Dihedral : 6.667 78.725 1881 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.74 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 0.08 (0.21), residues: 1689 helix: 0.99 (0.19), residues: 848 sheet: -0.80 (0.36), residues: 170 loop : -0.86 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 79 HIS 0.003 0.001 HIS C 94 PHE 0.023 0.001 PHE A 279 TYR 0.017 0.002 TYR E 402 ARG 0.005 0.000 ARG D 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TRP cc_start: 0.9336 (m100) cc_final: 0.9065 (m100) REVERT: A 139 TYR cc_start: 0.9485 (m-80) cc_final: 0.8987 (m-80) REVERT: A 150 ASN cc_start: 0.8826 (t0) cc_final: 0.8506 (m-40) REVERT: A 162 GLN cc_start: 0.9579 (tt0) cc_final: 0.9021 (tp-100) REVERT: A 176 LYS cc_start: 0.9479 (tptp) cc_final: 0.9162 (tppt) REVERT: A 227 LEU cc_start: 0.9304 (tt) cc_final: 0.8982 (tt) REVERT: A 229 PHE cc_start: 0.9215 (t80) cc_final: 0.8829 (t80) REVERT: A 233 ASP cc_start: 0.8912 (m-30) cc_final: 0.8659 (m-30) REVERT: A 259 TYR cc_start: 0.9107 (t80) cc_final: 0.8805 (t80) REVERT: A 260 ASP cc_start: 0.9213 (t0) cc_final: 0.8919 (t0) REVERT: A 291 LYS cc_start: 0.9338 (tptt) cc_final: 0.9056 (pttm) REVERT: B 32 LEU cc_start: 0.9633 (mm) cc_final: 0.9307 (pp) REVERT: B 36 LEU cc_start: 0.9616 (mm) cc_final: 0.8894 (mm) REVERT: B 57 TYR cc_start: 0.9249 (m-80) cc_final: 0.8988 (m-80) REVERT: B 90 MET cc_start: 0.8244 (mmp) cc_final: 0.7768 (tmm) REVERT: B 118 HIS cc_start: 0.9210 (m-70) cc_final: 0.8630 (m-70) REVERT: B 127 ASN cc_start: 0.9508 (m-40) cc_final: 0.8998 (m-40) REVERT: B 203 PHE cc_start: 0.9338 (t80) cc_final: 0.9081 (t80) REVERT: C 163 ASP cc_start: 0.8943 (m-30) cc_final: 0.8478 (p0) REVERT: C 244 MET cc_start: 0.8688 (tpp) cc_final: 0.8373 (tpt) REVERT: D 86 PHE cc_start: 0.9378 (t80) cc_final: 0.9134 (t80) REVERT: D 224 ASP cc_start: 0.9577 (t0) cc_final: 0.9152 (p0) REVERT: D 244 MET cc_start: 0.4951 (tpt) cc_final: 0.4706 (tpp) REVERT: E 44 PHE cc_start: 0.9059 (m-80) cc_final: 0.8629 (m-80) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2822 time to fit residues: 104.2789 Evaluate side-chains 181 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 134 optimal weight: 0.0010 chunk 56 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.046520 restraints weight = 87136.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047850 restraints weight = 62972.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.048885 restraints weight = 48910.259| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12579 Z= 0.164 Angle : 0.604 7.220 17252 Z= 0.304 Chirality : 0.043 0.255 2083 Planarity : 0.005 0.043 2235 Dihedral : 6.559 79.254 1881 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % 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: 0.11 (0.21), residues: 1689 helix: 1.01 (0.19), residues: 845 sheet: -0.63 (0.35), residues: 177 loop : -0.86 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP B 207 HIS 0.004 0.001 HIS D 94 PHE 0.025 0.001 PHE A 98 TYR 0.016 0.002 TYR A 41 ARG 0.005 0.000 ARG D 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.56 seconds wall clock time: 50 minutes 2.78 seconds (3002.78 seconds total)