Starting phenix.real_space_refine on Mon Apr 8 12:54:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/04_2024/8pql_17822_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/04_2024/8pql_17822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/04_2024/8pql_17822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/04_2024/8pql_17822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/04_2024/8pql_17822_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pql_17822/04_2024/8pql_17822_updated.pdb" } resolution = 3.76 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= 0.005 sd= 0.103 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 Zn 3 6.06 5 S 81 5.16 5 C 8638 2.51 5 N 2347 2.21 5 O 2484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 301": "OE1" <-> "OE2" Residue "H GLU 516": "OE1" <-> "OE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 37": "OD1" <-> "OD2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "G PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13553 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 170} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "E" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 592 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4249 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 573} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 15, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 217 Chain: "K" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 563 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "U" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 546 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4820 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 17, 'TRANS': 611} Chain breaks: 2 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 218 Chain: "D" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 680 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 697 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 89} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6399 SG CYS K 42 52.753 69.663 49.824 1.00 68.29 S ATOM 6415 SG CYS K 45 51.811 67.496 53.053 1.00 65.56 S ATOM 6634 SG CYS K 83 51.629 71.225 53.148 1.00 73.17 S ATOM 6563 SG CYS K 75 55.602 79.066 38.529 1.00 84.04 S ATOM 6719 SG CYS K 94 55.605 78.723 42.456 1.00 73.92 S ATOM 6474 SG CYS K 53 46.390 69.362 54.503 1.00 77.11 S ATOM 6493 SG CYS K 56 43.857 69.368 57.339 1.00 78.49 S ATOM 6519 SG CYS K 68 42.945 70.662 53.723 1.00 71.21 S Time building chain proxies: 7.05, per 1000 atoms: 0.52 Number of scatterers: 13553 At special positions: 0 Unit cell: (136.16, 148.074, 174.455, 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) Zn 3 29.99 S 81 16.00 O 2484 8.00 N 2347 7.00 C 8638 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N SY8 C 701 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.90 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 80 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 45 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 42 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 83 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" ND1 HIS K 77 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 75 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 94 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" ND1 HIS K 82 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 68 " Number of angles added : 6 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3516 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 8 sheets defined 46.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 142 through 154 Processing helix chain 'C' and resid 160 through 179 Processing helix chain 'E' and resid 23 through 33 Processing helix chain 'H' and resid 7 through 10 No H-bonds generated for 'chain 'H' and resid 7 through 10' Processing helix chain 'H' and resid 44 through 50 Processing helix chain 'H' and resid 54 through 63 Processing helix chain 'H' and resid 86 through 93 Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 119 through 126 removed outlier: 3.791A pdb=" N ASP H 126 " --> pdb=" O ALA H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 136 Processing helix chain 'H' and resid 152 through 158 Processing helix chain 'H' and resid 164 through 170 Processing helix chain 'H' and resid 185 through 192 removed outlier: 3.765A pdb=" N SER H 192 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 203 Processing helix chain 'H' and resid 217 through 224 Processing helix chain 'H' and resid 229 through 234 Processing helix chain 'H' and resid 241 through 257 Processing helix chain 'H' and resid 263 through 277 Processing helix chain 'H' and resid 315 through 329 Processing helix chain 'H' and resid 335 through 350 Processing helix chain 'H' and resid 355 through 371 removed outlier: 3.952A pdb=" N ASN H 359 " --> pdb=" O LYS H 355 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER H 370 " --> pdb=" O ASP H 366 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN H 371 " --> pdb=" O MET H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 394 removed outlier: 3.729A pdb=" N LEU H 383 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU H 384 " --> pdb=" O ALA H 380 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER H 385 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE H 386 " --> pdb=" O SER H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 426 Processing helix chain 'H' and resid 435 through 453 removed outlier: 4.018A pdb=" N LYS H 440 " --> pdb=" O LEU H 436 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA H 441 " --> pdb=" O GLN H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 474 Processing helix chain 'H' and resid 485 through 490 removed outlier: 3.552A pdb=" N VAL H 490 " --> pdb=" O LEU H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 496 No H-bonds generated for 'chain 'H' and resid 494 through 496' Processing helix chain 'H' and resid 508 through 517 Processing helix chain 'H' and resid 531 through 538 Processing helix chain 'H' and resid 541 through 550 removed outlier: 3.612A pdb=" N SER H 550 " --> pdb=" O LEU H 546 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 575 Processing helix chain 'H' and resid 581 through 583 No H-bonds generated for 'chain 'H' and resid 581 through 583' Processing helix chain 'H' and resid 586 through 597 Processing helix chain 'H' and resid 607 through 615 Processing helix chain 'K' and resid 54 through 57 No H-bonds generated for 'chain 'K' and resid 54 through 57' Processing helix chain 'K' and resid 82 through 88 Processing helix chain 'U' and resid 23 through 34 Processing helix chain 'U' and resid 56 through 58 No H-bonds generated for 'chain 'U' and resid 56 through 58' Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.769A pdb=" N THR A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.734A pdb=" N ASN A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 54 through 78 Processing helix chain 'A' and resid 87 through 104 removed outlier: 3.743A pdb=" N GLU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.513A pdb=" N HIS A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 201 through 228 Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 236 through 252 removed outlier: 3.793A pdb=" N ILE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.518A pdb=" N HIS A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 removed outlier: 4.063A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 Processing helix chain 'A' and resid 337 through 357 Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.699A pdb=" N SER A 366 " --> pdb=" O GLN A 362 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 410 through 424 removed outlier: 4.076A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 471 through 495 removed outlier: 3.993A pdb=" N ARG A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.920A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 removed outlier: 4.170A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.964A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 removed outlier: 4.254A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 67 through 82 removed outlier: 4.281A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 109 removed outlier: 3.541A pdb=" N MET D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 35 Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing sheet with id= A, first strand: chain 'C' and resid 60 through 63 Processing sheet with id= B, first strand: chain 'H' and resid 72 through 74 removed outlier: 6.605A pdb=" N VAL H 74 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU H 82 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'U' and resid 3 through 5 removed outlier: 3.929A pdb=" N VAL U 5 " --> pdb=" O ILE U 13 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE U 13 " --> pdb=" O VAL U 5 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'U' and resid 41 through 44 Processing sheet with id= E, first strand: chain 'A' and resid 561 through 566 Processing sheet with id= F, first strand: chain 'A' and resid 593 through 595 Processing sheet with id= G, first strand: chain 'D' and resid 28 through 32 Processing sheet with id= H, first strand: chain 'G' and resid 14 through 17 removed outlier: 6.531A pdb=" N ALA G 73 " --> pdb=" O MET G 6 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ARG G 8 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL G 75 " --> pdb=" O ARG G 8 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 5.37 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: 3393 1.33 - 1.46: 2942 1.46 - 1.58: 7363 1.58 - 1.70: 1 1.70 - 1.83: 129 Bond restraints: 13828 Sorted by residual: bond pdb=" C PRO C 48 " pdb=" N PRO C 49 " ideal model delta sigma weight residual 1.337 1.361 -0.025 1.06e-02 8.90e+03 5.50e+00 bond pdb=" CB PRO G 97 " pdb=" CG PRO G 97 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.08e+00 bond pdb=" N LEU C 125 " pdb=" CA LEU C 125 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.42e+00 bond pdb=" C PRO C 49 " pdb=" O PRO C 49 " ideal model delta sigma weight residual 1.239 1.215 0.023 1.27e-02 6.20e+03 3.38e+00 bond pdb=" CB GLN A 546 " pdb=" CG GLN A 546 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.12e+00 ... (remaining 13823 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.17: 355 106.17 - 113.15: 7614 113.15 - 120.13: 4724 120.13 - 127.11: 6004 127.11 - 134.10: 150 Bond angle restraints: 18847 Sorted by residual: angle pdb=" O PRO C 48 " pdb=" C PRO C 48 " pdb=" N PRO C 49 " ideal model delta sigma weight residual 121.15 118.66 2.49 4.70e-01 4.53e+00 2.82e+01 angle pdb=" CA PRO G 97 " pdb=" N PRO G 97 " pdb=" CD PRO G 97 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.77e+01 angle pdb=" N HIS K 80 " pdb=" CA HIS K 80 " pdb=" C HIS K 80 " ideal model delta sigma weight residual 110.35 104.99 5.36 1.38e+00 5.25e-01 1.51e+01 angle pdb=" C VAL H 99 " pdb=" N GLN H 100 " pdb=" CA GLN H 100 " ideal model delta sigma weight residual 121.14 114.45 6.69 1.75e+00 3.27e-01 1.46e+01 angle pdb=" CA LYS A 433 " pdb=" CB LYS A 433 " pdb=" CG LYS A 433 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 ... (remaining 18842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 7706 27.36 - 54.71: 522 54.71 - 82.07: 29 82.07 - 109.42: 10 109.42 - 136.78: 2 Dihedral angle restraints: 8269 sinusoidal: 2869 harmonic: 5400 Sorted by residual: dihedral pdb=" CA ASP C 102 " pdb=" C ASP C 102 " pdb=" N ASP C 103 " pdb=" CA ASP C 103 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA PRO A 154 " pdb=" C PRO A 154 " pdb=" N LEU A 155 " pdb=" CA LEU A 155 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" C1 SY8 C 701 " pdb=" C2 SY8 C 701 " pdb=" C3 SY8 C 701 " pdb=" C4 SY8 C 701 " ideal model delta sinusoidal sigma weight residual 57.79 -78.99 136.78 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 8266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1922 0.060 - 0.119: 280 0.119 - 0.179: 20 0.179 - 0.239: 0 0.239 - 0.299: 1 Chirality restraints: 2223 Sorted by residual: chirality pdb=" CG LEU A 559 " pdb=" CB LEU A 559 " pdb=" CD1 LEU A 559 " pdb=" CD2 LEU A 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE E 36 " pdb=" CA ILE E 36 " pdb=" CG1 ILE E 36 " pdb=" CG2 ILE E 36 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA HIS K 80 " pdb=" N HIS K 80 " pdb=" C HIS K 80 " pdb=" CB HIS K 80 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 2220 not shown) Planarity restraints: 2419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 138 " -0.078 5.00e-02 4.00e+02 1.16e-01 2.15e+01 pdb=" N PRO C 139 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 255 " -0.058 5.00e-02 4.00e+02 8.75e-02 1.22e+01 pdb=" N PRO A 256 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 71 " -0.052 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO G 72 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " -0.043 5.00e-02 4.00e+02 ... (remaining 2416 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 90 2.57 - 3.15: 10800 3.15 - 3.73: 20601 3.73 - 4.32: 25243 4.32 - 4.90: 42424 Nonbonded interactions: 99158 Sorted by model distance: nonbonded pdb=" OD2 ASP K 97 " pdb="ZN ZN K 202 " model vdw 1.986 2.230 nonbonded pdb=" O ILE U 61 " pdb=" OG SER U 65 " model vdw 2.119 2.440 nonbonded pdb=" O TYR C 57 " pdb=" OG1 THR C 172 " model vdw 2.232 2.440 nonbonded pdb=" O GLN E 49 " pdb=" OH TYR E 59 " model vdw 2.263 2.440 nonbonded pdb=" OE2 GLU A 208 " pdb=" OG SER A 258 " model vdw 2.267 2.440 ... (remaining 99153 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 'E' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 32 or (resid 33 through 34 and (name N \ or name CA or name C or name O or name CB )) or resid 35 or (resid 36 and (name \ N or name CA or name C or name O or name CB )) or resid 37 through 47 or resid \ 49 through 692 or resid 694)) selection = (chain 'U' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 26 or (resid 27 through 28 and (name \ N or name CA or name C or name O or name CB )) or resid 29 through 39 or (resid \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 47 or resid 49 through 51 or (resid 52 and (name N or name CA or name C or name \ O or name CB )) or resid 53 through 61 or (resid 62 through 64 and (name N or n \ ame CA or name C or name O or name CB )) or resid 65 through 69 or (resid 70 thr \ ough 73 and (name N or name CA or name C or name O or name CB )) or resid 75)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 11.780 Check model and map are aligned: 0.210 Set scattering table: 0.110 Process input model: 38.980 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 13828 Z= 0.219 Angle : 0.699 8.846 18847 Z= 0.364 Chirality : 0.042 0.299 2223 Planarity : 0.006 0.116 2418 Dihedral : 17.441 136.780 4752 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.54 % Allowed : 33.41 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.67 (0.20), residues: 1807 helix: 0.96 (0.18), residues: 914 sheet: -1.77 (0.57), residues: 92 loop : -2.02 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 27 HIS 0.009 0.001 HIS A 320 PHE 0.019 0.001 PHE A 364 TYR 0.023 0.001 TYR A 558 ARG 0.013 0.001 ARG K 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 344 time to evaluate : 1.360 Fit side-chains REVERT: U 27 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8351 (mttt) REVERT: A 37 ASP cc_start: 0.7354 (t0) cc_final: 0.7102 (t0) REVERT: A 297 MET cc_start: 0.7998 (ttm) cc_final: 0.7649 (ttm) REVERT: A 441 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8081 (ttmm) outliers start: 7 outliers final: 4 residues processed: 347 average time/residue: 0.2786 time to fit residues: 136.3041 Evaluate side-chains 341 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 337 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain A residue 622 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 46 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13828 Z= 0.196 Angle : 0.551 8.011 18847 Z= 0.282 Chirality : 0.040 0.210 2223 Planarity : 0.005 0.072 2418 Dihedral : 5.945 97.015 1959 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 5.75 % Allowed : 29.66 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.52 (0.21), residues: 1807 helix: 1.12 (0.18), residues: 913 sheet: -1.68 (0.58), residues: 92 loop : -1.99 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 517 HIS 0.006 0.001 HIS H 616 PHE 0.012 0.001 PHE A 350 TYR 0.015 0.001 TYR A 558 ARG 0.007 0.000 ARG H 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 344 time to evaluate : 1.555 Fit side-chains REVERT: H 178 LYS cc_start: 0.8295 (mmtp) cc_final: 0.8056 (mmtm) REVERT: H 319 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7473 (mtt-85) REVERT: H 388 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 37 ASP cc_start: 0.7413 (t0) cc_final: 0.7118 (t0) REVERT: A 393 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7538 (mptt) REVERT: A 396 ASP cc_start: 0.7408 (p0) cc_final: 0.7205 (p0) REVERT: A 441 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8139 (ttmm) REVERT: A 455 GLU cc_start: 0.7452 (tp30) cc_final: 0.6926 (mm-30) REVERT: D 82 ARG cc_start: 0.7017 (tpt90) cc_final: 0.6814 (tpt90) outliers start: 75 outliers final: 42 residues processed: 384 average time/residue: 0.2637 time to fit residues: 145.1886 Evaluate side-chains 388 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 344 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 319 ARG Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 540 HIS Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 75 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 55 optimal weight: 0.0060 chunk 129 optimal weight: 0.6980 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13828 Z= 0.164 Angle : 0.539 7.900 18847 Z= 0.274 Chirality : 0.040 0.162 2223 Planarity : 0.005 0.067 2418 Dihedral : 4.795 68.134 1954 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.13 % Allowed : 29.81 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.39 (0.21), residues: 1807 helix: 1.22 (0.18), residues: 911 sheet: -1.41 (0.60), residues: 85 loop : -1.95 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 33 HIS 0.004 0.001 HIS H 616 PHE 0.011 0.001 PHE A 350 TYR 0.012 0.001 TYR D 79 ARG 0.008 0.000 ARG H 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 349 time to evaluate : 1.327 Fit side-chains REVERT: H 178 LYS cc_start: 0.8286 (mmtp) cc_final: 0.8023 (mmtm) REVERT: H 244 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.6621 (mtm-85) REVERT: H 319 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7575 (mtt-85) REVERT: H 388 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7120 (mm-30) REVERT: U 27 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8196 (tptm) REVERT: A 37 ASP cc_start: 0.7441 (t0) cc_final: 0.7076 (t0) REVERT: A 247 GLU cc_start: 0.7264 (tm-30) cc_final: 0.7044 (tm-30) REVERT: A 251 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7340 (ttm-80) REVERT: A 396 ASP cc_start: 0.7451 (p0) cc_final: 0.7172 (p0) REVERT: A 415 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 438 MET cc_start: 0.7304 (mtm) cc_final: 0.7025 (mtm) REVERT: A 441 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8066 (ttmm) REVERT: A 454 GLU cc_start: 0.7789 (mp0) cc_final: 0.7490 (mp0) REVERT: A 457 MET cc_start: 0.7522 (tpp) cc_final: 0.7306 (tpp) REVERT: D 82 ARG cc_start: 0.7042 (tpt90) cc_final: 0.6803 (tpt90) outliers start: 67 outliers final: 43 residues processed: 385 average time/residue: 0.2604 time to fit residues: 145.2790 Evaluate side-chains 388 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 342 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 319 ARG Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 27 LYS Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 75 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 143 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13828 Z= 0.273 Angle : 0.585 8.622 18847 Z= 0.304 Chirality : 0.042 0.165 2223 Planarity : 0.005 0.066 2418 Dihedral : 4.933 61.055 1954 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 6.51 % Allowed : 29.50 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.58 (0.21), residues: 1807 helix: 1.12 (0.18), residues: 907 sheet: -1.72 (0.57), residues: 92 loop : -2.05 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 517 HIS 0.006 0.001 HIS H 616 PHE 0.018 0.002 PHE A 10 TYR 0.022 0.001 TYR D 79 ARG 0.007 0.000 ARG H 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 342 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: H 178 LYS cc_start: 0.8327 (mmtp) cc_final: 0.8078 (mmtm) REVERT: H 319 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7684 (mtt-85) REVERT: H 388 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7165 (mm-30) REVERT: K 97 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5737 (m-30) REVERT: A 37 ASP cc_start: 0.7520 (t0) cc_final: 0.7153 (t0) REVERT: A 251 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7326 (ttm-80) REVERT: A 415 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8175 (mm) REVERT: A 457 MET cc_start: 0.7550 (tpp) cc_final: 0.7177 (tpp) REVERT: A 598 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: D 82 ARG cc_start: 0.7056 (tpt90) cc_final: 0.6821 (tpt90) outliers start: 85 outliers final: 64 residues processed: 390 average time/residue: 0.2575 time to fit residues: 145.4258 Evaluate side-chains 394 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 326 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 319 ARG Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 516 GLU Chi-restraints excluded: chain H residue 565 SER Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 75 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 128 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN ** H 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13828 Z= 0.230 Angle : 0.573 8.511 18847 Z= 0.294 Chirality : 0.041 0.226 2223 Planarity : 0.005 0.067 2418 Dihedral : 4.882 59.609 1954 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 7.13 % Allowed : 28.97 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.59 (0.20), residues: 1807 helix: 1.11 (0.18), residues: 906 sheet: -1.77 (0.57), residues: 92 loop : -2.05 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 517 HIS 0.005 0.001 HIS H 616 PHE 0.015 0.001 PHE A 10 TYR 0.017 0.001 TYR D 79 ARG 0.006 0.000 ARG H 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 331 time to evaluate : 1.624 Fit side-chains REVERT: H 100 GLN cc_start: 0.8035 (pm20) cc_final: 0.7685 (pm20) REVERT: H 178 LYS cc_start: 0.8314 (mmtp) cc_final: 0.8045 (mmtm) REVERT: H 244 ARG cc_start: 0.7613 (mtt-85) cc_final: 0.7375 (mtm-85) REVERT: H 319 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7757 (mtt-85) REVERT: K 97 ASP cc_start: 0.6001 (OUTLIER) cc_final: 0.5749 (m-30) REVERT: A 37 ASP cc_start: 0.7522 (t0) cc_final: 0.7115 (t0) REVERT: A 251 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7393 (ttm-80) REVERT: A 438 MET cc_start: 0.7190 (mtm) cc_final: 0.6900 (mtm) REVERT: A 454 GLU cc_start: 0.7647 (mp0) cc_final: 0.7384 (mp0) REVERT: A 598 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: D 82 ARG cc_start: 0.7057 (tpt90) cc_final: 0.6834 (tpt90) outliers start: 93 outliers final: 68 residues processed: 386 average time/residue: 0.2529 time to fit residues: 142.1410 Evaluate side-chains 402 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 331 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 319 ARG Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 516 GLU Chi-restraints excluded: chain H residue 565 SER Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 75 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 101 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 0.0040 chunk 14 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 166 optimal weight: 0.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN H 187 HIS ** H 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13828 Z= 0.166 Angle : 0.554 9.431 18847 Z= 0.281 Chirality : 0.040 0.223 2223 Planarity : 0.005 0.067 2418 Dihedral : 4.667 55.930 1954 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 6.28 % Allowed : 30.27 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.42 (0.21), residues: 1807 helix: 1.25 (0.18), residues: 900 sheet: -1.63 (0.58), residues: 92 loop : -1.96 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 27 HIS 0.003 0.001 HIS H 616 PHE 0.012 0.001 PHE A 350 TYR 0.018 0.001 TYR A 558 ARG 0.005 0.000 ARG H 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 340 time to evaluate : 1.428 Fit side-chains REVERT: H 100 GLN cc_start: 0.8091 (pm20) cc_final: 0.7797 (pm20) REVERT: H 178 LYS cc_start: 0.8280 (mmtp) cc_final: 0.8017 (mmtm) REVERT: H 244 ARG cc_start: 0.7598 (mtt-85) cc_final: 0.7339 (mtt-85) REVERT: H 319 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7734 (mtt-85) REVERT: A 37 ASP cc_start: 0.7519 (t0) cc_final: 0.7113 (t0) REVERT: A 251 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7469 (ttm-80) REVERT: A 454 GLU cc_start: 0.7474 (mp0) cc_final: 0.7171 (mp0) REVERT: A 519 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7760 (pt) REVERT: A 598 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7227 (pm20) outliers start: 82 outliers final: 61 residues processed: 387 average time/residue: 0.2575 time to fit residues: 144.7894 Evaluate side-chains 403 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 339 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 105 HIS Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 319 ARG Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 565 SER Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 75 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 HIS ** H 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13828 Z= 0.235 Angle : 0.584 10.040 18847 Z= 0.299 Chirality : 0.042 0.224 2223 Planarity : 0.005 0.066 2418 Dihedral : 4.785 57.250 1954 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 6.44 % Allowed : 29.89 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1807 helix: 1.16 (0.18), residues: 904 sheet: -1.66 (0.58), residues: 92 loop : -2.03 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 33 HIS 0.005 0.001 HIS D 68 PHE 0.015 0.001 PHE A 10 TYR 0.020 0.001 TYR H 204 ARG 0.005 0.000 ARG H 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 334 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: H 178 LYS cc_start: 0.8302 (mmtp) cc_final: 0.8041 (mmtm) REVERT: H 244 ARG cc_start: 0.7689 (mtt-85) cc_final: 0.7451 (mtm110) REVERT: H 319 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7748 (mtt-85) REVERT: K 97 ASP cc_start: 0.6190 (OUTLIER) cc_final: 0.5876 (m-30) REVERT: A 37 ASP cc_start: 0.7531 (t0) cc_final: 0.7141 (t0) REVERT: A 251 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7427 (ttm-80) REVERT: A 454 GLU cc_start: 0.7750 (mp0) cc_final: 0.7508 (mp0) REVERT: A 598 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7217 (pm20) outliers start: 84 outliers final: 67 residues processed: 384 average time/residue: 0.2525 time to fit residues: 141.1879 Evaluate side-chains 408 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 338 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 319 ARG Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 516 GLU Chi-restraints excluded: chain H residue 565 SER Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 80 HIS Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 560 CYS Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 75 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 HIS ** H 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13828 Z= 0.214 Angle : 0.586 9.493 18847 Z= 0.298 Chirality : 0.042 0.251 2223 Planarity : 0.005 0.067 2418 Dihedral : 4.792 57.515 1954 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 6.13 % Allowed : 31.11 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.54 (0.21), residues: 1807 helix: 1.16 (0.18), residues: 905 sheet: -1.70 (0.57), residues: 92 loop : -2.04 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 27 HIS 0.004 0.001 HIS D 68 PHE 0.015 0.001 PHE A 10 TYR 0.019 0.001 TYR A 558 ARG 0.005 0.000 ARG H 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 346 time to evaluate : 1.537 Fit side-chains REVERT: H 178 LYS cc_start: 0.8299 (mmtp) cc_final: 0.8029 (mmtm) REVERT: H 244 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7445 (mtm110) REVERT: H 319 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7773 (mtt-85) REVERT: U 27 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7758 (mmtt) REVERT: A 37 ASP cc_start: 0.7552 (t0) cc_final: 0.7158 (t0) REVERT: A 251 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7474 (ttm-80) REVERT: A 517 TRP cc_start: 0.8272 (m100) cc_final: 0.7967 (m100) REVERT: A 598 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: G 94 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.8126 (p) outliers start: 80 outliers final: 69 residues processed: 395 average time/residue: 0.2444 time to fit residues: 140.8652 Evaluate side-chains 416 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 344 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 319 ARG Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 516 GLU Chi-restraints excluded: chain H residue 565 SER Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 80 HIS Chi-restraints excluded: chain K residue 94 CYS Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 0.0270 chunk 159 optimal weight: 0.2980 chunk 164 optimal weight: 0.0770 chunk 96 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 125 optimal weight: 0.0670 chunk 49 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 169 optimal weight: 0.4980 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13828 Z= 0.160 Angle : 0.579 10.420 18847 Z= 0.292 Chirality : 0.040 0.256 2223 Planarity : 0.005 0.066 2418 Dihedral : 4.905 80.755 1954 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.44 % Allowed : 33.18 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1807 helix: 1.33 (0.18), residues: 895 sheet: -1.60 (0.58), residues: 92 loop : -1.94 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 27 HIS 0.004 0.001 HIS H 95 PHE 0.013 0.001 PHE A 350 TYR 0.017 0.001 TYR H 470 ARG 0.004 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 335 time to evaluate : 1.407 Fit side-chains REVERT: H 244 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7385 (mtm110) REVERT: H 348 TYR cc_start: 0.7072 (m-80) cc_final: 0.6834 (m-10) REVERT: K 97 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5904 (m-30) REVERT: A 37 ASP cc_start: 0.7538 (t0) cc_final: 0.7083 (t0) REVERT: A 251 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7562 (ttm-80) REVERT: A 276 GLN cc_start: 0.7989 (pp30) cc_final: 0.7362 (mt0) REVERT: A 451 MET cc_start: 0.6832 (tmm) cc_final: 0.6616 (tmm) REVERT: A 598 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: G 94 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.8118 (p) outliers start: 58 outliers final: 46 residues processed: 369 average time/residue: 0.2464 time to fit residues: 132.4488 Evaluate side-chains 386 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 337 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 150 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN H 187 HIS ** H 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN A 397 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13828 Z= 0.207 Angle : 0.605 9.832 18847 Z= 0.307 Chirality : 0.042 0.281 2223 Planarity : 0.005 0.067 2418 Dihedral : 4.928 76.958 1954 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.44 % Allowed : 32.49 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.37 (0.21), residues: 1807 helix: 1.33 (0.18), residues: 894 sheet: -1.61 (0.57), residues: 92 loop : -1.95 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 517 HIS 0.007 0.001 HIS K 80 PHE 0.017 0.001 PHE A 350 TYR 0.017 0.001 TYR A 558 ARG 0.005 0.000 ARG H 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 350 time to evaluate : 1.387 Fit side-chains REVERT: H 244 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7445 (mtt-85) REVERT: H 348 TYR cc_start: 0.7155 (m-80) cc_final: 0.6944 (m-10) REVERT: U 27 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7738 (mmtt) REVERT: A 37 ASP cc_start: 0.7564 (t0) cc_final: 0.7140 (t0) REVERT: A 251 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7556 (ttm-80) REVERT: A 276 GLN cc_start: 0.8016 (pp30) cc_final: 0.7363 (mt0) REVERT: A 430 VAL cc_start: 0.8406 (m) cc_final: 0.8143 (p) REVERT: A 454 GLU cc_start: 0.7651 (mp0) cc_final: 0.7444 (mp0) REVERT: A 598 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: G 94 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8125 (p) outliers start: 58 outliers final: 54 residues processed: 386 average time/residue: 0.2590 time to fit residues: 144.7329 Evaluate side-chains 400 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 344 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 137 PHE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 255 PHE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 393 MET Chi-restraints excluded: chain H residue 394 LEU Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain K residue 79 PHE Chi-restraints excluded: chain K residue 97 ASP Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 124 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 187 HIS H 334 HIS H 368 GLN ** H 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN A 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.136007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115531 restraints weight = 25875.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117940 restraints weight = 14500.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118887 restraints weight = 9883.739| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 13828 Z= 0.297 Angle : 0.835 59.163 18847 Z= 0.471 Chirality : 0.044 0.739 2223 Planarity : 0.005 0.067 2418 Dihedral : 4.929 76.995 1954 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 4.67 % Allowed : 32.41 % Favored : 62.91 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.32 % 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: -0.37 (0.21), residues: 1807 helix: 1.33 (0.18), residues: 894 sheet: -1.61 (0.58), residues: 92 loop : -1.96 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 517 HIS 0.005 0.001 HIS H 334 PHE 0.019 0.001 PHE A 10 TYR 0.015 0.001 TYR D 79 ARG 0.004 0.000 ARG H 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.13 seconds wall clock time: 62 minutes 21.32 seconds (3741.32 seconds total)