Starting phenix.real_space_refine on Mon Jul 22 03:42:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9g_36986/07_2024/8k9g_36986.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9g_36986/07_2024/8k9g_36986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9g_36986/07_2024/8k9g_36986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9g_36986/07_2024/8k9g_36986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9g_36986/07_2024/8k9g_36986.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9g_36986/07_2024/8k9g_36986.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 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 90 5.49 5 S 46 5.16 5 C 10498 2.51 5 N 2810 2.21 5 O 3315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 284": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 16759 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "H" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "A" Number of atoms: 3684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3684 Classifications: {'peptide': 455} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 429} Chain breaks: 1 Chain: "B" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3695 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 10.03, per 1000 atoms: 0.60 Number of scatterers: 16759 At special positions: 0 Unit cell: (85.28, 148.72, 172.64, 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 46 16.00 P 90 15.00 O 3315 8.00 N 2810 7.00 C 10498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.21 Conformation dependent library (CDL) restraints added in 3.1 seconds 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 20 sheets defined 40.0% alpha, 14.1% beta 2 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 5.96 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 97 through 105 removed outlier: 4.412A pdb=" N ILE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.511A pdb=" N ARG A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.727A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.641A pdb=" N GLY A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.605A pdb=" N GLU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.869A pdb=" N ASN A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 7.102A pdb=" N ASP B 16 " --> pdb=" O PRO B 12 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 4.451A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.576A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.765A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 146 through 158 removed outlier: 4.127A pdb=" N SER B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.900A pdb=" N LEU B 194 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.582A pdb=" N LEU B 203 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.789A pdb=" N ILE B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N HIS B 225 " --> pdb=" O ASP B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.620A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.588A pdb=" N GLU B 237 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.666A pdb=" N ILE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.580A pdb=" N ASP B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.656A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS B 366 " --> pdb=" O ARG B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.850A pdb=" N GLU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'E' and resid 22 through 30 Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.766A pdb=" N LYS E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 97 through 106 removed outlier: 3.839A pdb=" N ILE E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 132 removed outlier: 3.600A pdb=" N ASN E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 205 through 215 removed outlier: 4.034A pdb=" N GLN E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 247 No H-bonds generated for 'chain 'E' and resid 245 through 247' Processing helix chain 'E' and resid 248 through 265 Processing helix chain 'E' and resid 322 through 326 Processing helix chain 'E' and resid 331 through 351 Processing helix chain 'E' and resid 367 through 374 Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 477 through 491 removed outlier: 3.700A pdb=" N ALA E 483 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN E 484 " --> pdb=" O LEU E 480 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS E 485 " --> pdb=" O ARG E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 4.191A pdb=" N TYR E 505 " --> pdb=" O ALA E 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 65 through 70 removed outlier: 4.339A pdb=" N LYS F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 89 removed outlier: 3.640A pdb=" N LEU F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 removed outlier: 3.861A pdb=" N VAL F 113 " --> pdb=" O ASN F 109 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 109 through 114' Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 149 through 156 Processing helix chain 'F' and resid 190 through 194 removed outlier: 3.859A pdb=" N LEU F 194 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.536A pdb=" N LEU F 203 " --> pdb=" O VAL F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 233 removed outlier: 3.803A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 257 through 280 Processing helix chain 'F' and resid 353 through 366 removed outlier: 3.638A pdb=" N GLN F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS F 366 " --> pdb=" O ARG F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 385 Processing helix chain 'F' and resid 421 through 438 removed outlier: 3.776A pdb=" N GLU F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 449 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.876A pdb=" N LYS A 270 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.745A pdb=" N VAL A 92 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 282 removed outlier: 6.583A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 441 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 420 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 396 through 398 Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.714A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.051A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS B 4 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 59 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE B 118 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.612A pdb=" N VAL B 334 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 404 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 403 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 188 Processing sheet with id=AB1, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.578A pdb=" N ALA B 292 " --> pdb=" O TYR B 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AB3, first strand: chain 'E' and resid 397 through 398 removed outlier: 5.580A pdb=" N LYS F 167 " --> pdb=" O MET F 414 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET F 414 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU F 169 " --> pdb=" O GLY F 412 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 4 " --> pdb=" O PHE F 411 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS F 413 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N TYR E 6 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N SER F 415 " --> pdb=" O TYR E 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.956A pdb=" N ILE E 12 " --> pdb=" O CYS E 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS E 20 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 95 removed outlier: 3.782A pdb=" N GLY E 45 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL E 141 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 303 through 304 removed outlier: 6.570A pdb=" N CYS E 279 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N HIS E 360 " --> pdb=" O CYS E 279 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU E 281 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL E 357 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL E 386 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE E 359 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 388 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA E 361 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 425 through 426 removed outlier: 4.018A pdb=" N VAL E 426 " --> pdb=" O SER E 431 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 31 through 33 removed outlier: 5.891A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS F 4 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU F 61 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE F 6 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL F 63 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER F 8 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ILE F 95 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE F 60 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU F 97 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE F 62 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 285 through 286 removed outlier: 7.060A pdb=" N PHE F 291 " --> pdb=" O ALA F 325 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA F 325 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR F 293 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE F 323 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 285 through 286 removed outlier: 7.060A pdb=" N PHE F 291 " --> pdb=" O ALA F 325 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA F 325 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR F 293 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE F 323 " --> pdb=" O TYR F 293 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 334 " --> pdb=" O LYS F 328 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU F 402 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE F 401 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 403 " --> pdb=" O ILE F 391 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 207 through 210 553 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 8.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4067 1.33 - 1.45: 3844 1.45 - 1.57: 9190 1.57 - 1.69: 176 1.69 - 1.81: 70 Bond restraints: 17347 Sorted by residual: bond pdb=" N VAL B 395 " pdb=" CA VAL B 395 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.08e-02 8.57e+03 1.18e+01 bond pdb=" N THR F 11 " pdb=" CA THR F 11 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.26e+00 bond pdb=" N THR B 11 " pdb=" CA THR B 11 " ideal model delta sigma weight residual 1.462 1.490 -0.029 9.50e-03 1.11e+04 9.21e+00 bond pdb=" C THR B 11 " pdb=" N PRO B 12 " ideal model delta sigma weight residual 1.331 1.354 -0.023 7.90e-03 1.60e+04 8.25e+00 bond pdb=" C THR F 11 " pdb=" N PRO F 12 " ideal model delta sigma weight residual 1.332 1.355 -0.023 8.20e-03 1.49e+04 7.75e+00 ... (remaining 17342 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.49: 618 105.49 - 112.70: 9002 112.70 - 119.92: 6420 119.92 - 127.14: 7431 127.14 - 134.35: 375 Bond angle restraints: 23846 Sorted by residual: angle pdb=" N ASP B 386 " pdb=" CA ASP B 386 " pdb=" C ASP B 386 " ideal model delta sigma weight residual 111.71 105.69 6.02 1.15e+00 7.56e-01 2.74e+01 angle pdb=" CB ARG B 276 " pdb=" CG ARG B 276 " pdb=" CD ARG B 276 " ideal model delta sigma weight residual 111.30 122.10 -10.80 2.30e+00 1.89e-01 2.20e+01 angle pdb=" CA LYS B 280 " pdb=" CB LYS B 280 " pdb=" CG LYS B 280 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CA LYS F 400 " pdb=" CB LYS F 400 " pdb=" CG LYS F 400 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" CA LYS B 309 " pdb=" CB LYS B 309 " pdb=" CG LYS B 309 " ideal model delta sigma weight residual 114.10 123.00 -8.90 2.00e+00 2.50e-01 1.98e+01 ... (remaining 23841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8179 17.94 - 35.88: 1485 35.88 - 53.82: 534 53.82 - 71.77: 157 71.77 - 89.71: 33 Dihedral angle restraints: 10388 sinusoidal: 5059 harmonic: 5329 Sorted by residual: dihedral pdb=" C5' G G 5 " pdb=" C4' G G 5 " pdb=" C3' G G 5 " pdb=" O3' G G 5 " ideal model delta sinusoidal sigma weight residual 147.00 102.65 44.35 1 8.00e+00 1.56e-02 4.27e+01 dihedral pdb=" O4' G G 5 " pdb=" C4' G G 5 " pdb=" C3' G G 5 " pdb=" C2' G G 5 " ideal model delta sinusoidal sigma weight residual 24.00 -16.06 40.06 1 8.00e+00 1.56e-02 3.52e+01 dihedral pdb=" C3' G G 5 " pdb=" C4' G G 5 " pdb=" O4' G G 5 " pdb=" C1' G G 5 " ideal model delta sinusoidal sigma weight residual -2.00 33.77 -35.77 1 8.00e+00 1.56e-02 2.83e+01 ... (remaining 10385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2519 0.122 - 0.244: 87 0.244 - 0.366: 2 0.366 - 0.488: 2 0.488 - 0.610: 5 Chirality restraints: 2615 Sorted by residual: chirality pdb=" P DA H 36 " pdb=" OP1 DA H 36 " pdb=" OP2 DA H 36 " pdb=" O5' DA H 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" P DA H 31 " pdb=" OP1 DA H 31 " pdb=" OP2 DA H 31 " pdb=" O5' DA H 31 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" P DA D 36 " pdb=" OP1 DA D 36 " pdb=" OP2 DA D 36 " pdb=" O5' DA D 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 2612 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 15 " 0.024 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ASP F 15 " -0.087 2.00e-02 2.50e+03 pdb=" O ASP F 15 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP F 16 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 272 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ALA F 272 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA F 272 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE F 273 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 276 " -0.240 9.50e-02 1.11e+02 1.07e-01 7.11e+00 pdb=" NE ARG F 276 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG F 276 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG F 276 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 276 " -0.008 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1578 2.74 - 3.28: 15893 3.28 - 3.82: 28524 3.82 - 4.36: 31846 4.36 - 4.90: 53629 Nonbonded interactions: 131470 Sorted by model distance: nonbonded pdb=" OG1 THR A 71 " pdb=" OE2 GLU B 426 " model vdw 2.201 2.440 nonbonded pdb=" NE1 TRP B 219 " pdb=" OE1 GLU B 398 " model vdw 2.220 2.520 nonbonded pdb=" O PRO A 404 " pdb=" OH TYR B 416 " model vdw 2.245 2.440 nonbonded pdb=" O3' DA D 36 " pdb=" NH2 ARG B 263 " model vdw 2.246 2.520 nonbonded pdb=" OG1 THR E 71 " pdb=" OE2 GLU F 426 " model vdw 2.250 2.440 ... (remaining 131465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 1 through 151 or resid 204 through 507)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.670 Check model and map are aligned: 0.170 Set scattering table: 0.140 Process input model: 51.930 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 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 : 0.005 0.062 17347 Z= 0.303 Angle : 0.852 11.726 23846 Z= 0.471 Chirality : 0.059 0.610 2615 Planarity : 0.006 0.107 2712 Dihedral : 21.185 89.707 6942 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.25 % Allowed : 35.10 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.18), residues: 1799 helix: -0.88 (0.19), residues: 633 sheet: -0.46 (0.32), residues: 271 loop : -1.92 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 219 HIS 0.008 0.001 HIS A 251 PHE 0.039 0.002 PHE E 313 TYR 0.024 0.002 TYR F 154 ARG 0.013 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.6470 (t80) outliers start: 4 outliers final: 2 residues processed: 161 average time/residue: 0.3570 time to fit residues: 83.2865 Evaluate side-chains 96 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 278 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 147 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 151 ASN B 183 ASN B 258 ASN B 262 GLN ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 446 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17347 Z= 0.234 Angle : 0.611 8.687 23846 Z= 0.325 Chirality : 0.043 0.195 2615 Planarity : 0.004 0.066 2712 Dihedral : 18.856 87.283 3180 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.07 % Allowed : 33.31 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.19), residues: 1799 helix: 0.11 (0.20), residues: 635 sheet: -0.54 (0.31), residues: 289 loop : -1.68 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 373 HIS 0.004 0.001 HIS E 329 PHE 0.017 0.001 PHE F 273 TYR 0.015 0.001 TYR E 346 ARG 0.005 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 106 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7331 (p0) outliers start: 66 outliers final: 23 residues processed: 164 average time/residue: 0.3229 time to fit residues: 76.8991 Evaluate side-chains 109 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 34 CYS Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 389 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17347 Z= 0.376 Angle : 0.698 9.682 23846 Z= 0.367 Chirality : 0.044 0.181 2615 Planarity : 0.005 0.063 2712 Dihedral : 19.154 96.912 3174 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.61 % Allowed : 31.71 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1799 helix: 0.18 (0.20), residues: 642 sheet: -0.70 (0.31), residues: 289 loop : -1.58 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 370 HIS 0.005 0.001 HIS B 225 PHE 0.015 0.002 PHE B 158 TYR 0.016 0.002 TYR B 392 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 93 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7325 (mtt90) REVERT: B 3 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7440 (p0) REVERT: E 131 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.6986 (p0) REVERT: E 504 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7515 (ptmt) outliers start: 91 outliers final: 45 residues processed: 173 average time/residue: 0.3148 time to fit residues: 79.7528 Evaluate side-chains 133 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 84 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 504 LYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 0.0040 chunk 171 optimal weight: 0.8980 chunk 181 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17347 Z= 0.175 Angle : 0.588 8.766 23846 Z= 0.307 Chirality : 0.042 0.159 2615 Planarity : 0.004 0.053 2712 Dihedral : 19.034 98.998 3174 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.52 % Allowed : 33.13 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1799 helix: 0.48 (0.21), residues: 644 sheet: -0.52 (0.31), residues: 294 loop : -1.50 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 370 HIS 0.022 0.001 HIS A 251 PHE 0.019 0.001 PHE F 273 TYR 0.013 0.001 TYR E 346 ARG 0.014 0.000 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 96 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7331 (pp) REVERT: E 131 ASN cc_start: 0.7176 (OUTLIER) cc_final: 0.6896 (p0) REVERT: E 150 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7770 (t80) REVERT: E 364 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8005 (mpp-170) outliers start: 57 outliers final: 27 residues processed: 147 average time/residue: 0.3076 time to fit residues: 67.3321 Evaluate side-chains 117 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 86 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17347 Z= 0.326 Angle : 0.660 9.630 23846 Z= 0.343 Chirality : 0.043 0.192 2615 Planarity : 0.004 0.052 2712 Dihedral : 19.219 98.599 3174 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.18 % Allowed : 31.03 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1799 helix: 0.44 (0.21), residues: 643 sheet: -0.68 (0.31), residues: 283 loop : -1.51 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 370 HIS 0.006 0.001 HIS A 251 PHE 0.020 0.002 PHE B 135 TYR 0.015 0.002 TYR E 346 ARG 0.005 0.001 ARG F 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 89 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7262 (pp) REVERT: E 131 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.7120 (p0) REVERT: F 345 MET cc_start: 0.7950 (pmm) cc_final: 0.7723 (pmm) outliers start: 84 outliers final: 54 residues processed: 165 average time/residue: 0.3073 time to fit residues: 75.2002 Evaluate side-chains 142 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 86 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.9990 chunk 163 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS B 226 GLN ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 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 17347 Z= 0.193 Angle : 0.589 10.824 23846 Z= 0.305 Chirality : 0.042 0.193 2615 Planarity : 0.004 0.051 2712 Dihedral : 19.120 98.991 3174 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.39 % Allowed : 33.25 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1799 helix: 0.59 (0.21), residues: 643 sheet: -0.57 (0.31), residues: 283 loop : -1.49 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 33 HIS 0.003 0.001 HIS A 251 PHE 0.018 0.001 PHE B 135 TYR 0.012 0.001 TYR E 346 ARG 0.004 0.000 ARG E 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 94 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7326 (pp) REVERT: E 364 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8262 (mpp-170) outliers start: 55 outliers final: 42 residues processed: 145 average time/residue: 0.3059 time to fit residues: 66.3494 Evaluate side-chains 129 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 85 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17347 Z= 0.166 Angle : 0.577 11.514 23846 Z= 0.297 Chirality : 0.041 0.198 2615 Planarity : 0.004 0.049 2712 Dihedral : 19.006 96.328 3174 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.39 % Allowed : 32.82 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1799 helix: 0.67 (0.21), residues: 645 sheet: -0.50 (0.30), residues: 306 loop : -1.50 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 33 HIS 0.009 0.001 HIS A 251 PHE 0.017 0.001 PHE B 135 TYR 0.010 0.001 TYR E 346 ARG 0.004 0.000 ARG E 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 94 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7307 (pp) REVERT: B 287 MET cc_start: 0.5697 (tpp) cc_final: 0.5416 (tpt) REVERT: E 364 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8281 (mpp-170) outliers start: 55 outliers final: 40 residues processed: 142 average time/residue: 0.3167 time to fit residues: 67.3767 Evaluate side-chains 132 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 90 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17347 Z= 0.170 Angle : 0.572 12.467 23846 Z= 0.294 Chirality : 0.041 0.203 2615 Planarity : 0.004 0.050 2712 Dihedral : 18.951 94.591 3174 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.02 % Allowed : 33.25 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1799 helix: 0.73 (0.21), residues: 645 sheet: -0.47 (0.31), residues: 306 loop : -1.46 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 33 HIS 0.004 0.001 HIS A 251 PHE 0.021 0.001 PHE B 135 TYR 0.009 0.001 TYR E 346 ARG 0.009 0.000 ARG F 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 95 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7303 (pp) REVERT: A 434 SER cc_start: 0.7614 (OUTLIER) cc_final: 0.7378 (p) REVERT: E 364 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8269 (mpp-170) outliers start: 49 outliers final: 41 residues processed: 138 average time/residue: 0.3001 time to fit residues: 62.3725 Evaluate side-chains 132 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 88 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.6980 chunk 158 optimal weight: 8.9990 chunk 168 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17347 Z= 0.192 Angle : 0.584 13.269 23846 Z= 0.299 Chirality : 0.041 0.209 2615 Planarity : 0.004 0.049 2712 Dihedral : 18.982 93.001 3174 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.27 % Allowed : 33.07 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1799 helix: 0.75 (0.21), residues: 646 sheet: -0.48 (0.31), residues: 306 loop : -1.46 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 33 HIS 0.004 0.001 HIS A 251 PHE 0.018 0.001 PHE B 135 TYR 0.009 0.001 TYR E 346 ARG 0.005 0.000 ARG F 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 88 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7310 (pp) REVERT: A 434 SER cc_start: 0.7579 (OUTLIER) cc_final: 0.7374 (p) REVERT: B 287 MET cc_start: 0.5529 (tpp) cc_final: 0.5021 (tpt) REVERT: E 150 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7727 (t80) REVERT: E 364 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8337 (mpp-170) outliers start: 53 outliers final: 44 residues processed: 135 average time/residue: 0.3219 time to fit residues: 64.8796 Evaluate side-chains 136 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 88 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.4980 chunk 84 optimal weight: 0.0870 chunk 124 optimal weight: 0.2980 chunk 187 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 0.0870 chunk 91 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17347 Z= 0.152 Angle : 0.576 13.267 23846 Z= 0.293 Chirality : 0.041 0.201 2615 Planarity : 0.004 0.049 2712 Dihedral : 18.858 91.548 3174 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.10 % Allowed : 33.87 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1799 helix: 0.80 (0.21), residues: 645 sheet: -0.25 (0.32), residues: 285 loop : -1.41 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 33 HIS 0.014 0.001 HIS B 225 PHE 0.014 0.001 PHE B 135 TYR 0.008 0.001 TYR F 293 ARG 0.005 0.000 ARG F 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 287 MET cc_start: 0.5504 (tpp) cc_final: 0.5051 (tpt) REVERT: E 150 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7581 (t80) REVERT: E 364 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8216 (mpp-170) outliers start: 34 outliers final: 27 residues processed: 119 average time/residue: 0.3170 time to fit residues: 55.8284 Evaluate side-chains 114 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 183 ASN Chi-restraints excluded: chain F residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.0070 chunk 137 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.0170 chunk 131 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059412 restraints weight = 130914.380| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 5.30 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17347 Z= 0.185 Angle : 0.578 13.177 23846 Z= 0.296 Chirality : 0.041 0.204 2615 Planarity : 0.004 0.049 2712 Dihedral : 18.880 89.825 3174 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.10 % Allowed : 33.81 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1799 helix: 0.83 (0.21), residues: 646 sheet: -0.29 (0.32), residues: 285 loop : -1.40 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 33 HIS 0.014 0.001 HIS B 225 PHE 0.014 0.001 PHE B 135 TYR 0.008 0.001 TYR E 346 ARG 0.005 0.000 ARG F 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.08 seconds wall clock time: 54 minutes 29.48 seconds (3269.48 seconds total)